From 5eb1e8d970f895c4380640ea0b5d376705ddc7c7 Mon Sep 17 00:00:00 2001
From: Hazen Babcock <hbabcock@mac.com>
Date: Thu, 27 Oct 2016 17:20:59 -0400
Subject: [PATCH 01/17] Make tracker into a C library.

---
 storm_analysis/sa_utilities/std_analysis.py |  3 +-
 storm_analysis/sa_utilities/tracker.c       | 32 +++++++++----------
 storm_analysis/sa_utilities/tracker_c.py    | 34 +++++++++++++++++++++
 3 files changed, 51 insertions(+), 18 deletions(-)
 create mode 100644 storm_analysis/sa_utilities/tracker_c.py

diff --git a/storm_analysis/sa_utilities/std_analysis.py b/storm_analysis/sa_utilities/std_analysis.py
index ad126e4a..f9a03783 100644
--- a/storm_analysis/sa_utilities/std_analysis.py
+++ b/storm_analysis/sa_utilities/std_analysis.py
@@ -195,7 +195,8 @@ def standardAnalysis(find_peaks, data_file, mlist_file, parameters):
 # Does the frame-to-frame tracking.
 def tracking(mol_list_filename, parameters):
     [min_z, max_z] = params.getZRange(parameters)
-    proc_params = [src_dir + "tracker",
+    proc_params = ["python",
+                   src_dir + "tracker_c",
                    mol_list_filename,
                    parameters.descriptor,
                    str(parameters.radius),
diff --git a/storm_analysis/sa_utilities/tracker.c b/storm_analysis/sa_utilities/tracker.c
index 20222bec..3b790fdd 100644
--- a/storm_analysis/sa_utilities/tracker.c
+++ b/storm_analysis/sa_utilities/tracker.c
@@ -13,16 +13,12 @@
  *
  * 01/14
  *
+ * Changed into a C library.
  *
- * Hazen
- * 
- * Compilation instructions:
+ * 10/16
  *
- * Linux:
- *  gcc tracker.c -o tracker -lm
+ * Hazen
  *
- * Windows:
- *  gcc tracker.c -o tracker
  */
 
 
@@ -43,7 +39,7 @@ struct track_elt* createTrackObject(float *, int, int);
 int addObject(float *, float, int, int, int);
 void freeTrack(struct track_elt *);
 void cullTracks(FILE *, int, int);
-
+int tracker(int, const char **);
 
 /* Structures */
 struct track_elt
@@ -138,7 +134,7 @@ struct track_elt* createTrackObject(float *object_data, int track_id, int molecu
 
 int addObject(float *object_data, float r_sqr_max, int track_id, int molecule_id, int frame_no)
 {
-  int i, found = 0, *object_data_int;
+  int found = 0, *object_data_int;
   float dx, dy, weight;
   struct track_elt *cur, *last, *new_track, *new_object;
 
@@ -268,7 +264,7 @@ void freeTrack(struct track_elt *start)
 
 void cullTracks(FILE *mlist, int cull_frame, int save_track_ids)
 {
-  int i, culled, *object_data_int, first_cat;
+  int culled, *object_data_int, first_cat;
   float *object_data;
   struct track_elt *cur, *last, *to_save;
 
@@ -337,7 +333,7 @@ void cullTracks(FILE *mlist, int cull_frame, int save_track_ids)
 
 
 /*
- * Main
+ * tracker
  *
  * Descriptor is a string of the form "02110311" that 
  * describes the different frames.
@@ -348,14 +344,14 @@ void cullTracks(FILE *mlist, int cull_frame, int save_track_ids)
  *   ...
  *
  */
-
-int main(int argc, const char *argv[])
+int tracker(int argc, const char *argv[])
 {
-  char version[5],tmp[2];
+  char tmp[2];
   int i, cur_frame, track_number, last_frame;
-  int molecules, temp, desc_len, cur_desc, save_track_ids;
+  int molecules, desc_len, cur_desc, save_track_ids;
   int *object_data_int, *descriptor;
   float max_radius, zmin, zmax, object_data[OBJECT_DATA_SIZE];
+  size_t n_read;
   FILE *mlist;
 
   if (argc < 6){
@@ -376,7 +372,7 @@ int main(int argc, const char *argv[])
   }
 
   fseek(mlist, MOLECULES, SEEK_SET);
-  fread(&molecules, sizeof(int), 1, mlist);
+  n_read = fread(&molecules, sizeof(int), 1, mlist);
   printf("Molecules: %d (%s)\n", molecules, argv[1]);
 
   printf("Descriptor: %s\n", argv[2]);
@@ -413,7 +409,7 @@ int main(int argc, const char *argv[])
       //printf(" (%f, %f, %f)\n", object_data[X], object_data[Y], object_data[Z]);
     }
     fseeko64(mlist, DATA + OBJECT_DATA_SIZE*DATUM_SIZE*(long long)i, SEEK_SET);
-    fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, mlist);
+    n_read = fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, mlist);
     cur_frame = object_data_int[FRAME];
     cur_desc = descriptor[(cur_frame-1)%desc_len];
 
@@ -454,6 +450,8 @@ int main(int argc, const char *argv[])
   printf("Found %d tracks\n", track_number);
 
   fclose(mlist);
+
+  return 0;
 }
 
 
diff --git a/storm_analysis/sa_utilities/tracker_c.py b/storm_analysis/sa_utilities/tracker_c.py
new file mode 100644
index 00000000..2bbb037e
--- /dev/null
+++ b/storm_analysis/sa_utilities/tracker_c.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+#
+# Python interface to the C tracker library. Note that this
+# library uses static variables so it is not thread safe.
+#
+# Hazen 10/16
+#
+
+import ctypes
+import os
+
+import storm_analysis.sa_library.loadclib as loadclib
+
+ctracker = loadclib.loadCLibrary(os.path.dirname(__file__), "tracker")
+
+ctracker.tracker.argtypes = [ctypes.c_int,
+                             ctypes.c_void_p]
+
+def tracker(mlist_filename, descriptor, radius, zmin, zmax, save_track_id = 0):
+    argc = 7
+    argv = (ctypes.c_char_p * argc)()
+    argv[:] = ["tracker",
+               mlist_filename,
+               descriptor,
+               str(radius),
+               str(zmin),
+               str(zmax),
+               str(save_track_id)]
+    ctracker.tracker(argc, argv)
+
+if (__name__ == "__main__"):
+    import sys
+    
+    tracker(*sys.argv[1:])

From a36a89b99287997af736044ffd3e5d2055c8981f Mon Sep 17 00:00:00 2001
From: Hazen Babcock <hbabcock@mac.com>
Date: Thu, 27 Oct 2016 17:58:01 -0400
Subject: [PATCH 02/17] Replace standalone C programs with C libraries that are
 called from Python.

---
 .../sa_utilities/apply-drift-correction.c     | 23 ++++++------
 .../sa_utilities/apply_drift_correction_c.py  | 30 +++++++++++++++
 storm_analysis/sa_utilities/avemlist.c        | 20 ++++++----
 storm_analysis/sa_utilities/avemlist_c.py     | 29 +++++++++++++++
 storm_analysis/sa_utilities/compile_linux.sh  | 20 ++++++++--
 storm_analysis/sa_utilities/fitz.c            | 28 ++++++++------
 storm_analysis/sa_utilities/fitz_c.py         | 37 +++++++++++++++++++
 storm_analysis/sa_utilities/std_analysis.py   | 11 ++++--
 storm_analysis/sa_utilities/tracker.c         |  1 -
 storm_analysis/sa_utilities/tracker_c.py      |  8 ++--
 10 files changed, 163 insertions(+), 44 deletions(-)
 create mode 100644 storm_analysis/sa_utilities/apply_drift_correction_c.py
 create mode 100644 storm_analysis/sa_utilities/avemlist_c.py
 create mode 100644 storm_analysis/sa_utilities/fitz_c.py

diff --git a/storm_analysis/sa_utilities/apply-drift-correction.c b/storm_analysis/sa_utilities/apply-drift-correction.c
index f9ce2de9..234ba771 100644
--- a/storm_analysis/sa_utilities/apply-drift-correction.c
+++ b/storm_analysis/sa_utilities/apply-drift-correction.c
@@ -2,16 +2,13 @@
  * Applies drift correction to a molecule list,
  * works in place.
  *
- * Hazen
  * 12/11
  *
- * Compilation instructions:
+ * Changed into a C library.
  *
- * Linux:
- *  gcc apply-drift-correction.c -o apply-drift-correction
+ * 10/16
  *
- * Windows:
- *  gcc apply-drift-correction.c -o apply-drift-correction
+ * Hazen
  */
 
 
@@ -23,21 +20,23 @@
 #include "insight.h"
 
 
+int applyDriftCorrection(int, const char **);
+
 /*
- * Main
+ * applyDriftCorrection
  *
  * mlist - the molecule list file
  * drift - the drift correction file (in i3 standard format).
  *
  */
-
-int main(int argc, const char *argv[])
+int applyDriftCorrection(int argc, const char *argv[])
 {
   int i,cur_frame,frames,molecules,temp;
   int *object_data_int;
   char str[100];
   float *dx,*dy,*dz;
   float object_data[OBJECT_DATA_SIZE];
+  size_t n_read;
   FILE *mlist_fp,*drift_fp;
 
   if (argc != 3){
@@ -55,7 +54,7 @@ int main(int argc, const char *argv[])
   // Figure out how many molecules there are to process.
   mlist_fp = fopen(argv[1], "rb+");
   fseek(mlist_fp, MOLECULES, SEEK_SET);
-  fread(&molecules, sizeof(int), 1, mlist_fp);
+  n_read = fread(&molecules, sizeof(int), 1, mlist_fp);
   printf(" Molecules: %d\n", molecules);
 
   // Determine size of drift correction file & load into memory.
@@ -92,7 +91,7 @@ int main(int argc, const char *argv[])
       printf(" Processing molecule %d in frame %d (apply-drift-correction)\n", i, cur_frame);
     }
     fseeko64(mlist_fp, DATA + OBJECT_DATA_SIZE*DATUM_SIZE*(long long)i, SEEK_SET);
-    fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, mlist_fp);
+    n_read = fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, mlist_fp);
     cur_frame = object_data_int[FRAME]-1;
 
     // range checking
@@ -117,6 +116,8 @@ int main(int argc, const char *argv[])
   free(dy);
   free(dz);
   fclose(mlist_fp);
+
+  return 0;
 }
 
 
diff --git a/storm_analysis/sa_utilities/apply_drift_correction_c.py b/storm_analysis/sa_utilities/apply_drift_correction_c.py
new file mode 100644
index 00000000..1e35a3c3
--- /dev/null
+++ b/storm_analysis/sa_utilities/apply_drift_correction_c.py
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+#
+# Python interface to the C apply_drift_correction library. Note that this
+# library uses static variables so it is not thread safe.
+#
+# Hazen 10/16
+#
+
+import ctypes
+import os
+
+import storm_analysis.sa_library.loadclib as loadclib
+
+adc = loadclib.loadCLibrary(os.path.dirname(__file__), "apply-drift-correction")
+
+adc.applyDriftCorrection.argtypes = [ctypes.c_int,
+                                     ctypes.c_void_p]
+
+def applyDriftCorrection(mlist_filename, drift_filename):
+    argc = 3
+    argv = (ctypes.c_char_p * argc)()
+    argv[:] = ["apply-drift-correction",
+               mlist_filename,
+               drift_filename]
+    adc.applyDriftCorrection(argc, argv)
+
+if (__name__ == "__main__"):
+    import sys
+    
+    applyDriftCorrection(*sys.argv[1:])
diff --git a/storm_analysis/sa_utilities/avemlist.c b/storm_analysis/sa_utilities/avemlist.c
index c012da9a..ee04b25c 100644
--- a/storm_analysis/sa_utilities/avemlist.c
+++ b/storm_analysis/sa_utilities/avemlist.c
@@ -29,7 +29,7 @@
 
 /* Functions */
 void averageTrack(FILE *, FILE *, int, int);
-
+int avemlist(int, const char **);
 
 /* These are as in the insight.h file */
 static int average_flag[] = {AVERAGE,      /* XO */
@@ -61,6 +61,7 @@ void averageTrack(FILE *input_mlist, FILE *output_mlist, int molecule, int visit
 {
   int i,*object_data_int,elements,track_id;
   float weight, total_weight;
+  size_t n_read;
   float average_data[OBJECT_DATA_SIZE], object_data[OBJECT_DATA_SIZE];
   
   elements = 1;
@@ -68,7 +69,7 @@ void averageTrack(FILE *input_mlist, FILE *output_mlist, int molecule, int visit
 
   // load object data
   fseeko64(input_mlist, DATA + OBJECT_DATA_SIZE*DATUM_SIZE*(long long)molecule, SEEK_SET);
-  fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, input_mlist);
+  n_read = fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, input_mlist);
   for(i=0;i<(OBJECT_DATA_SIZE);i++){
     average_data[i] = object_data[i];
   }
@@ -94,7 +95,7 @@ void averageTrack(FILE *input_mlist, FILE *output_mlist, int molecule, int visit
     molecule = object_data_int[LINK];
     // printf(" %d\n", molecule);
     fseeko64(input_mlist, DATA + OBJECT_DATA_SIZE*DATUM_SIZE*(long long)molecule, SEEK_SET);
-    fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, input_mlist);  
+    n_read = fread(&object_data, sizeof(float), OBJECT_DATA_SIZE, input_mlist);  
     
     if (TESTING){
       if(track_id != object_data_int[FITI]){
@@ -142,11 +143,12 @@ void averageTrack(FILE *input_mlist, FILE *output_mlist, int molecule, int visit
  *
  */
 
-int main(int argc, const char *argv[])
+int avemlist(int argc, const char *argv[])
 {
   int i, last_frame, molecules, tracks, unvisited;
   char header[DATA];
   int object_data[OBJECT_DATA_SIZE];
+  size_t n_read;
   FILE *input_mlist, *output_mlist;
 
   if (argc != 3){
@@ -171,15 +173,15 @@ int main(int argc, const char *argv[])
     exit(0);
   }
 
-  fread(&header, sizeof(char), DATA, input_mlist);
+  n_read = fread(&header, sizeof(char), DATA, input_mlist);
   fwrite(&header, sizeof(char), DATA, output_mlist);
 
   fseek(input_mlist, MOLECULES, SEEK_SET);
-  fread(&molecules, sizeof(int), 1, input_mlist);
+  n_read = fread(&molecules, sizeof(int), 1, input_mlist);
   // printf("Molecules: %d\n", molecules);
 
   fseek(input_mlist, DATA, SEEK_SET);
-  fread(&object_data, sizeof(int), OBJECT_DATA_SIZE, input_mlist);
+  n_read = fread(&object_data, sizeof(int), OBJECT_DATA_SIZE, input_mlist);
   unvisited = object_data[VISITED];
   // printf("Unvisited: %d\n", unvisited);
 
@@ -193,7 +195,7 @@ int main(int argc, const char *argv[])
       printf("Processing molecule %d (avemlist)\n", i);
     }
     fseeko64(input_mlist, DATA + OBJECT_DATA_SIZE*DATUM_SIZE*(long long)i, SEEK_SET);
-    fread(&object_data, sizeof(int), OBJECT_DATA_SIZE, input_mlist);
+    n_read = fread(&object_data, sizeof(int), OBJECT_DATA_SIZE, input_mlist);
     if (last_frame != object_data[FRAME]){
       fflush(input_mlist);
       last_frame = object_data[FRAME];
@@ -217,6 +219,8 @@ int main(int argc, const char *argv[])
 
   fclose(input_mlist);
   fclose(output_mlist);
+
+  return 0;
 }
 
 
diff --git a/storm_analysis/sa_utilities/avemlist_c.py b/storm_analysis/sa_utilities/avemlist_c.py
new file mode 100644
index 00000000..f1f7e63d
--- /dev/null
+++ b/storm_analysis/sa_utilities/avemlist_c.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+#
+# Python interface to the C avemlist library.
+#
+# Hazen 10/16
+#
+
+import ctypes
+import os
+
+import storm_analysis.sa_library.loadclib as loadclib
+
+c_avemlist = loadclib.loadCLibrary(os.path.dirname(__file__), "avemlist")
+
+c_avemlist.avemlist.argtypes = [ctypes.c_int,
+                                ctypes.c_void_p]
+
+def avemlist(input_filename, output_filename):
+    argc = 3
+    argv = (ctypes.c_char_p * argc)()
+    argv[:] = ["avemlist",
+               input_filename,
+               output_filename]
+    c_avemlist.avemlist(argc, argv)
+
+if (__name__ == "__main__"):
+    import sys
+    
+    avemlist(*sys.argv[1:])
diff --git a/storm_analysis/sa_utilities/compile_linux.sh b/storm_analysis/sa_utilities/compile_linux.sh
index 3ba4e3c1..5c590dab 100644
--- a/storm_analysis/sa_utilities/compile_linux.sh
+++ b/storm_analysis/sa_utilities/compile_linux.sh
@@ -1,6 +1,18 @@
 #!/bin/bash
 
-gcc tracker.c -o tracker -lc -lm
-gcc apply-drift-correction.c -o apply-drift-correction -lc
-gcc fitz.c -o fitz -lc -lm
-gcc avemlist.c -o avemlist -lc -lm
+gcc -fPIC -g -c -Wall -O3 tracker.c
+gcc -shared -Wl,-soname,tracker.so.1 -o tracker.so.1.0.1 tracker.o
+ln -s tracker.so.1.0.1 tracker.so
+
+gcc -fPIC -g -c -Wall -O3 apply-drift-correction.c
+gcc -shared -Wl,-soname,apply-drift-correction.so.1 -o apply-drift-correction.so.1.0.1 apply-drift-correction.o
+ln -s apply-drift-correction.so.1.0.1 apply-drift-correction.so
+
+gcc -fPIC -g -c -Wall -O3 fitz.c
+gcc -shared -Wl,-soname,fitz.so.1 -o fitz.so.1.0.1 fitz.o
+ln -s fitz.so.1.0.1 fitz.so
+
+gcc -fPIC -g -c -Wall -O3 avemlist.c
+gcc -shared -Wl,-soname,avemlist.so.1 -o avemlist.so.1.0.1 avemlist.o
+ln -s avemlist.so.1.0.1 avemlist.so
+
diff --git a/storm_analysis/sa_utilities/fitz.c b/storm_analysis/sa_utilities/fitz.c
index dc38226e..dc642dce 100644
--- a/storm_analysis/sa_utilities/fitz.c
+++ b/storm_analysis/sa_utilities/fitz.c
@@ -1,17 +1,14 @@
 /*
- * 07/11
- *
  * Performs z fit based on wx, wy on a Insight3 file.
  * Works "in place".
  *
+ * 07/11
  *
- * Hazen
- * 
- * Compilation instructions:
+ * Changed into a C library.
  *
- * Linux:
- *  gcc fitz.c -o fitz -lm
+ * 10/16
  *
+ * Hazen
  */
 
 
@@ -29,6 +26,10 @@
 double *wx_curve;
 double *wy_curve;
 
+void initWxWy(double *, double *);
+float findBestZ(double, double, double);
+int fitz(int, const char **);
+
 
 /*
  * Initialize wx, wy pre-calculated array curves.
@@ -96,7 +97,7 @@ float findBestZ(double wx, double wy, double cutoff)
 
 
 /*
- * Main
+ * fitz
  *
  * i3_file - insight3 file on which to perform z calculations.
  * cut_off - distance cutoff
@@ -106,7 +107,7 @@ float findBestZ(double wx, double wy, double cutoff)
  * Expects calibration curves & molecule widths to be in nm.
  */
 
-int main(int argc, const char *argv[])
+int fitz(int argc, const char *argv[])
 {
   int i,bad_cat,molecules,offset;
   float w,a,z;
@@ -114,6 +115,7 @@ int main(int argc, const char *argv[])
   double wx,wy;
   double wx_params[7];
   double wy_params[7];
+  size_t n_read;
   FILE *mlist;
 
   if (argc == 1){
@@ -137,7 +139,7 @@ int main(int argc, const char *argv[])
   }
 
   fseek(mlist, MOLECULES, SEEK_SET);
-  fread(&molecules, sizeof(int), 1, mlist);
+  n_read = fread(&molecules, sizeof(int), 1, mlist);
   printf("Molecules: %d\n", molecules);
 
   initWxWy(wx_params, wy_params);
@@ -151,10 +153,10 @@ int main(int argc, const char *argv[])
     offset = DATA + i*OBJECT_DATA_SIZE*DATUM_SIZE;
 
     fseeko64(mlist, offset+WIDTH*DATUM_SIZE, SEEK_SET);
-    fread(&w, sizeof(float), 1, mlist);
+    n_read = fread(&w, sizeof(float), 1, mlist);
 
     fseeko64(mlist, offset+ASPECT*DATUM_SIZE, SEEK_SET);
-    fread(&a, sizeof(float), 1, mlist);
+    n_read = fread(&a, sizeof(float), 1, mlist);
 
     wx = sqrt(sqrt(w*w/a));
     wy = sqrt(sqrt(w*w*a));
@@ -181,6 +183,8 @@ int main(int argc, const char *argv[])
   free(wx_curve);
   free(wy_curve);
   fclose(mlist);
+
+  return 0;
 }
 
 
diff --git a/storm_analysis/sa_utilities/fitz_c.py b/storm_analysis/sa_utilities/fitz_c.py
new file mode 100644
index 00000000..36233b67
--- /dev/null
+++ b/storm_analysis/sa_utilities/fitz_c.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+#
+# Python interface to the C fitz library. Note that this
+# library uses static variables so it is not thread safe.
+#
+# Hazen 10/16
+#
+
+import ctypes
+import os
+
+import storm_analysis.sa_library.loadclib as loadclib
+
+c_fitz = loadclib.loadCLibrary(os.path.dirname(__file__), "fitz")
+
+c_fitz.fitz.argtypes = [ctypes.c_int,
+                        ctypes.c_void_p]
+
+def fitz(i3_filename, cut_off, wx_params, wy_params):
+    argc = 17
+    argv = (ctypes.c_char_p * argc)()
+    argv[0] = "fitz"
+    argv[1] = i3_filename
+    argv[2] = str(cut_off)
+    for i in range(7):
+        argv[i+3] = str(wx_params[i])
+        argv[i+10] = str(wy_params[i])
+    c_fitz.fitz(argc, argv)
+
+if (__name__ == "__main__"):
+    import sys
+
+    if(len(sys.argv) != 17):
+        print("fitz_c.py requires 16 arguments")
+        exit()
+    
+    fitz(sys.argv[1], sys.argv[2], sys.argv[3:10], sys.argv[10:17])
diff --git a/storm_analysis/sa_utilities/std_analysis.py b/storm_analysis/sa_utilities/std_analysis.py
index f9a03783..dc9d2be5 100644
--- a/storm_analysis/sa_utilities/std_analysis.py
+++ b/storm_analysis/sa_utilities/std_analysis.py
@@ -21,7 +21,8 @@
 
 # Averages all the molecules in a track into a single molecule.
 def averaging(mol_list_filename, ave_list_filename):
-    proc_params = [src_dir + "avemlist",
+    proc_params = ["python",
+                   src_dir + "avemlist_c.py",
                    mol_list_filename,
                    ave_list_filename]
     subprocess.call(proc_params)
@@ -56,7 +57,8 @@ def driftCorrection(list_files, parameters):
 
     if (os.path.exists(drift_name)):
         for list_file in list_files:
-            proc_params = [src_dir + "apply-drift-correction",
+            proc_params = ["python",
+                           src_dir + "apply_drift_correction_c.py",
                            list_file,
                            drift_name]
             subprocess.call(proc_params)
@@ -196,7 +198,7 @@ def standardAnalysis(find_peaks, data_file, mlist_file, parameters):
 def tracking(mol_list_filename, parameters):
     [min_z, max_z] = params.getZRange(parameters)
     proc_params = ["python",
-                   src_dir + "tracker_c",
+                   src_dir + "tracker_c.py",
                    mol_list_filename,
                    parameters.descriptor,
                    str(parameters.radius),
@@ -213,7 +215,8 @@ def zFitting(mol_list_filename, parameters):
     else:
         wx_str = list(map(str, params.getWidthParams(parameters, "x")))
         wy_str = list(map(str, params.getWidthParams(parameters, "y")))
-    proc_params = [src_dir + "fitz",
+    proc_params = ["python",
+                   src_dir + "fitz_c.py",
                    mol_list_filename, 
                    str(parameters.cutoff)] + wx_str + wy_str
     subprocess.call(proc_params)
diff --git a/storm_analysis/sa_utilities/tracker.c b/storm_analysis/sa_utilities/tracker.c
index 3b790fdd..23648784 100644
--- a/storm_analysis/sa_utilities/tracker.c
+++ b/storm_analysis/sa_utilities/tracker.c
@@ -18,7 +18,6 @@
  * 10/16
  *
  * Hazen
- *
  */
 
 
diff --git a/storm_analysis/sa_utilities/tracker_c.py b/storm_analysis/sa_utilities/tracker_c.py
index 2bbb037e..cf3f28f2 100644
--- a/storm_analysis/sa_utilities/tracker_c.py
+++ b/storm_analysis/sa_utilities/tracker_c.py
@@ -11,10 +11,10 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-ctracker = loadclib.loadCLibrary(os.path.dirname(__file__), "tracker")
+c_tracker = loadclib.loadCLibrary(os.path.dirname(__file__), "tracker")
 
-ctracker.tracker.argtypes = [ctypes.c_int,
-                             ctypes.c_void_p]
+c_tracker.tracker.argtypes = [ctypes.c_int,
+                              ctypes.c_void_p]
 
 def tracker(mlist_filename, descriptor, radius, zmin, zmax, save_track_id = 0):
     argc = 7
@@ -26,7 +26,7 @@ def tracker(mlist_filename, descriptor, radius, zmin, zmax, save_track_id = 0):
                str(zmin),
                str(zmax),
                str(save_track_id)]
-    ctracker.tracker(argc, argv)
+    c_tracker.tracker(argc, argv)
 
 if (__name__ == "__main__"):
     import sys

From 2d7803b9bdae6d5f0d01e025138306565dcb2bc3 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 10:00:53 -0400
Subject: [PATCH 03/17] Basic setup.py

---
 __init__.py |   1 -
 setup.py    | 115 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 115 insertions(+), 1 deletion(-)
 delete mode 100644 __init__.py
 create mode 100644 setup.py

diff --git a/__init__.py b/__init__.py
deleted file mode 100644
index 013e4b7e..00000000
--- a/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-#!/usr/bin/python
diff --git a/setup.py b/setup.py
new file mode 100644
index 00000000..c59c426a
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from setuptools import setup, find_packages
+from distutils.core import Extension
+
+import numpy
+
+version = "1.0"
+description = "Read and write image data from and to TIFF files."
+long_description = ""
+
+def get_c_extensions():
+    extensions = [#Extension("", ["./storm_analysis/fista/fista_decon_utilities.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/fista/fista_fft.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_library/matched_filter.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_library/grid.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  Extension("", ["./storm_analysis/sa_library/multi_fit.c"],
+                            include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_library/ia_utilities.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/dbscan/dbscan.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/dbscan/kdtree.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/decon_storm/mlem_sparse.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sCMOS/scmos_utilities.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/fista_lib.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_storm.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_sse.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_general.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_common.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea_common.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_gpu.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_utilities/fitz.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_utilities/tracker.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_utilities/avemlist.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/sa_utilities/apply-drift-correction.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/frc/frc.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/simulator/draw_gaussians.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/simulator/zernike.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/spliner/cubic_spline.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/spliner/multi_fit_core.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/spliner/cubic_fit.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  #Extension("", ["./storm_analysis/rolling_ball_bgr/rolling_ball_lib.c"],
+                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+                  ]
+
+                  return extensions
+
+setup(
+    name='storm_analysis',
+    version=version,
+    description=description,
+    long_description=long_description,
+    author='Hazen Babcock',
+    author_email='hbabcock at fas.harvard.edu',
+    url='https://github.com/ZhuangLab/storm-analysis',
+
+    zip_safe=False,
+    packages=find_packages(),
+
+    ext_modules=get_c_extensions(),
+    package_data={
+        #'sample': ['package_data.dat'],
+        # If any package contains *.txt or *.rst files, include them:
+        #'': ['*.txt', '*.rst'],
+        # And include any *.msg files found in the 'hello' package, too:
+        #'hello': ['*.msg'],
+    },
+    exclude_package_data={
+        #'': ['README.txt']
+    },
+    include_package_data=True,
+
+    requires=['numpy (>=1.8.2)', 'setuptools'],
+    
+    license="",  
+    keywords='storm,microscopy',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Developers',
+        'License :: OSI Approved :: BSD License',
+        "Programming Language :: C",
+        "Programming Language :: Python :: 2",
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.4',
+    ],
+)
\ No newline at end of file

From f31e02bb02880c1b98288c889249e98a823f5485 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 10:58:22 -0400
Subject: [PATCH 04/17] Add some mechanism to load C extension

---
 .gitignore                                  |  2 +
 setup.py                                    | 90 +++++++--------------
 storm_analysis/sa_library/grid_c.py         |  2 +-
 storm_analysis/sa_library/ia_utilities_c.py |  2 +-
 storm_analysis/sa_library/loadclib.py       | 38 ++++++---
 storm_analysis/sa_library/multi_fit_c.py    |  2 +-
 6 files changed, 65 insertions(+), 71 deletions(-)

diff --git a/.gitignore b/.gitignore
index baf65ba6..17aee38f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,8 @@
 #############
 
 *.py[co]
+*.egg-info
+build/
 
 #############
 ## Emacs
diff --git a/setup.py b/setup.py
index c59c426a..893b879b 100644
--- a/setup.py
+++ b/setup.py
@@ -11,67 +11,39 @@
 long_description = ""
 
 def get_c_extensions():
-    extensions = [#Extension("", ["./storm_analysis/fista/fista_decon_utilities.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/fista/fista_fft.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_library/matched_filter.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_library/grid.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  Extension("", ["./storm_analysis/sa_library/multi_fit.c"],
-                            include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_library/ia_utilities.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/dbscan/dbscan.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/dbscan/kdtree.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/decon_storm/mlem_sparse.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sCMOS/scmos_utilities.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/fista_lib.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_storm.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_sse.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_general.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_common.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea_common.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_gpu.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_utilities/fitz.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_utilities/tracker.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_utilities/avemlist.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/sa_utilities/apply-drift-correction.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/frc/frc.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/simulator/draw_gaussians.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/simulator/zernike.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/spliner/cubic_spline.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/spliner/multi_fit_core.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/spliner/cubic_fit.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
-                  #Extension("", ["./storm_analysis/rolling_ball_bgr/rolling_ball_lib.c"],
-                  #          include_dirs=[], library_dirs=[], extra_link_args=[], extra_compile_args=[]),
+    extensions = [#Extension("", ["./storm_analysis/fista/fista_decon_utilities.c"], ),
+                  #Extension("", ["./storm_analysis/fista/fista_fft.c"], ),
+                  #Extension("", ["./storm_analysis/sa_library/matched_filter.c"], ),
+                  Extension("storm_analysis.sa_library._grid", ["./storm_analysis/sa_library/grid.c"], ),
+                  Extension("storm_analysis.sa_library._multi_fit", ["./storm_analysis/sa_library/multi_fit.c"],
+                            libraries=["lapack"]),
+                  Extension("storm_analysis.sa_library._ia_utilities", ["./storm_analysis/sa_library/ia_utilities.c"]),
+                  #Extension("", ["./storm_analysis/dbscan/dbscan.c"], ),
+                  #Extension("", ["./storm_analysis/dbscan/kdtree.c"], ),
+                  #Extension("", ["./storm_analysis/decon_storm/mlem_sparse.c"], ),
+                  #Extension("", ["./storm_analysis/sCMOS/scmos_utilities.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/fista_lib.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_storm.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_sse.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_general.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_common.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea_common.c"], ),
+                  #Extension("", ["./storm_analysis/L1H/homotopy_gpu.c"], ),
+                  #Extension("", ["./storm_analysis/sa_utilities/fitz.c"], ),
+                  #Extension("", ["./storm_analysis/sa_utilities/tracker.c"], ),
+                  #Extension("", ["./storm_analysis/sa_utilities/avemlist.c"], ),
+                  #Extension("", ["./storm_analysis/sa_utilities/apply-drift-correction.c"], ),
+                  #Extension("", ["./storm_analysis/frc/frc.c"], ),
+                  #Extension("", ["./storm_analysis/simulator/draw_gaussians.c"], ),
+                  #Extension("", ["./storm_analysis/simulator/zernike.c"], ),
+                  #Extension("", ["./storm_analysis/spliner/cubic_spline.c"], ),
+                  #Extension("", ["./storm_analysis/spliner/multi_fit_core.c"], ),
+                  #Extension("", ["./storm_analysis/spliner/cubic_fit.c"], ),
+                  #Extension("", ["./storm_analysis/rolling_ball_bgr/rolling_ball_lib.c"], ),
                   ]
 
-                  return extensions
+    return extensions
 
 setup(
     name='storm_analysis',
diff --git a/storm_analysis/sa_library/grid_c.py b/storm_analysis/sa_library/grid_c.py
index 94264bca..2e1953be 100644
--- a/storm_analysis/sa_library/grid_c.py
+++ b/storm_analysis/sa_library/grid_c.py
@@ -15,7 +15,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-grid = loadclib.loadCLibrary(os.path.dirname(__file__), "grid")
+grid = loadclib.loadCLibrary("storm_analysis.sa_library", "_grid")
 
 # Function specifications
 grid.grid2D.argtypes = [ndpointer(dtype=numpy.int32),
diff --git a/storm_analysis/sa_library/ia_utilities_c.py b/storm_analysis/sa_library/ia_utilities_c.py
index 9550cdcf..256675d2 100644
--- a/storm_analysis/sa_library/ia_utilities_c.py
+++ b/storm_analysis/sa_library/ia_utilities_c.py
@@ -13,7 +13,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-util = loadclib.loadCLibrary(os.path.dirname(__file__), "ia_utilities")
+util = loadclib.loadCLibrary("storm_analysis.sa_library", "_ia_utilities")
 
 # C interface definition
 util.findLocalMaxima.argtypes = [ndpointer(dtype=numpy.float64),
diff --git a/storm_analysis/sa_library/loadclib.py b/storm_analysis/sa_library/loadclib.py
index 2bc50e3f..d8031b2b 100644
--- a/storm_analysis/sa_library/loadclib.py
+++ b/storm_analysis/sa_library/loadclib.py
@@ -7,18 +7,38 @@
 
 import ctypes
 import sys
+import os
+import re
 
-def loadCLibrary(directory, library):
+import storm_analysis
 
-    if (directory == ""):
-        directory = "./"
-    else:
-        directory += "/"
 
-    if (sys.platform == "win32"):
-        return ctypes.cdll.LoadLibrary(directory + library + ".dll")
-    else:
-        return ctypes.cdll.LoadLibrary(directory + library + ".so")
+def loadCLibrary(package, library):
+
+	# Something like /usr/lib/python3.5/site-packages/storm_analysis
+	module_path = os.path.dirname(os.path.dirname(os.path.abspath(storm_analysis.__file__)))
+
+	# Something like /usr/lib/python3.5/site-packages/storm_analysis/sa_library/
+	lib_path = os.path.join(module_path, package.replace(".", os.path.sep))
+	files = os.listdir(lib_path)
+
+	lib_extension = "so"
+	if (sys.platform == "win32"):
+		lib_extension = "dll"
+
+	# Something like '_ia_utilities.*\.so'
+	r = re.compile('{}.*\.{}'.format(library, lib_extension))
+
+	lib_filename = list(filter(r.match, files))
+
+	if len(lib_filename) < 1:
+		raise Exception("Can't find the library {} in the module {} "
+						"located in the storm_analysis package at {}".format(library, package, module_path))
+
+	# Something like _ia_utilities.cpython-35m-x86_64-linux-gnu.so
+	lib_filename = lib_filename[0]
+
+	return ctypes.cdll.LoadLibrary(os.path.join(lib_path, lib_filename))
 
 #
 # The MIT License
diff --git a/storm_analysis/sa_library/multi_fit_c.py b/storm_analysis/sa_library/multi_fit_c.py
index 96990e3a..132ff5e8 100644
--- a/storm_analysis/sa_library/multi_fit_c.py
+++ b/storm_analysis/sa_library/multi_fit_c.py
@@ -29,7 +29,7 @@
 import storm_analysis.sa_library.ia_utilities_c as util_c
 import storm_analysis.sa_library.loadclib as loadclib
 
-multi = loadclib.loadCLibrary(os.path.dirname(__file__), "multi_fit")
+multi = loadclib.loadCLibrary("storm_analysis.sa_library", "_multi_fit")
 
 # C interface definition
 multi.getError.restype = c_double

From b73bf7eeec269fc77e987e73720343e2969836dd Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 11:27:16 -0400
Subject: [PATCH 05/17] More extension

---
 setup.py                                      | 29 ++++++++++++++++---
 storm_analysis/sa_library/matched_filter_c.py |  2 +-
 2 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index 893b879b..fcd82c6d 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import platform
+import os
+import sys
+
 from setuptools import setup, find_packages
 from distutils.core import Extension
 
@@ -11,13 +15,30 @@
 long_description = ""
 
 def get_c_extensions():
+
+    include_dirs = [os.path.join(sys.prefix, "include")]
+    library_dirs = []
+
+    if platform.system() == 'Windows':
+        include_dirs += [os.environ['LIBRARY_INC']]
+        library_dirs += [os.environ['LIBRARY_LIB']]
+    elif platform.system() == 'Linux':
+        include_dirs += []
+        library_dirs += []
+    elif platform.system() == 'Darwin':
+        include_dirs += []
+        library_dirs += []
+
     extensions = [#Extension("", ["./storm_analysis/fista/fista_decon_utilities.c"], ),
                   #Extension("", ["./storm_analysis/fista/fista_fft.c"], ),
-                  #Extension("", ["./storm_analysis/sa_library/matched_filter.c"], ),
-                  Extension("storm_analysis.sa_library._grid", ["./storm_analysis/sa_library/grid.c"], ),
+                  Extension("storm_analysis.sa_library._matched_filter", ["./storm_analysis/sa_library/matched_filter.c"],
+                            libraries=library_dirs + ["fftw3"], include_dirs=include_dirs + []),
+                  Extension("storm_analysis.sa_library._grid", ["./storm_analysis/sa_library/grid.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
                   Extension("storm_analysis.sa_library._multi_fit", ["./storm_analysis/sa_library/multi_fit.c"],
-                            libraries=["lapack"]),
-                  Extension("storm_analysis.sa_library._ia_utilities", ["./storm_analysis/sa_library/ia_utilities.c"]),
+                            libraries=library_dirs + ["lapack"], include_dirs=include_dirs + []),
+                  Extension("storm_analysis.sa_library._ia_utilities", ["./storm_analysis/sa_library/ia_utilities.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
                   #Extension("", ["./storm_analysis/dbscan/dbscan.c"], ),
                   #Extension("", ["./storm_analysis/dbscan/kdtree.c"], ),
                   #Extension("", ["./storm_analysis/decon_storm/mlem_sparse.c"], ),
diff --git a/storm_analysis/sa_library/matched_filter_c.py b/storm_analysis/sa_library/matched_filter_c.py
index 24fe7d07..fffc7407 100644
--- a/storm_analysis/sa_library/matched_filter_c.py
+++ b/storm_analysis/sa_library/matched_filter_c.py
@@ -13,7 +13,7 @@
 import storm_analysis.sa_library.loadclib as loadclib
 import storm_analysis.sa_library.recenter_psf as recenterPSF
 
-m_filter = loadclib.loadCLibrary(os.path.dirname(__file__), "matched_filter")
+m_filter = loadclib.loadCLibrary("storm_analysis.sa_library", "_matched_filter")
 
 m_filter.cleanup.argtypes = [ctypes.c_void_p]
 m_filter.convolve.argtypes = [ctypes.c_void_p,

From 82b4c341e93d04a7ead42d69f5eed4b3f1a68b05 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 12:10:54 -0400
Subject: [PATCH 06/17] More extensions

---
 setup.py                                      | 87 +++++++++++++------
 storm_analysis/L1H/homotopy_c.py              |  2 +-
 storm_analysis/L1H/homotopy_imagea_c.py       |  2 +-
 storm_analysis/dbscan/dbscan_c.py             |  4 +-
 storm_analysis/decon_storm/mlem_c.py          |  2 +-
 .../fista/fista_decon_utilities_c.py          |  2 +-
 storm_analysis/fista/fista_fft_c.py           |  2 +-
 storm_analysis/frc/frc_c.py                   |  2 +-
 .../rolling_ball_bgr/rolling_ball_lib_c.py    |  2 +-
 storm_analysis/sCMOS/scmos_utilities_c.py     |  2 +-
 storm_analysis/simulator/drawgaussians.py     |  2 +-
 storm_analysis/simulator/zernike_c.py         |  2 +-
 storm_analysis/spliner/cubic_fit_c.py         |  2 +-
 storm_analysis/spliner/cubic_spline_c.py      |  6 +-
 14 files changed, 77 insertions(+), 42 deletions(-)

diff --git a/setup.py b/setup.py
index fcd82c6d..ab948ffe 100644
--- a/setup.py
+++ b/setup.py
@@ -29,8 +29,11 @@ def get_c_extensions():
         include_dirs += []
         library_dirs += []
 
-    extensions = [#Extension("", ["./storm_analysis/fista/fista_decon_utilities.c"], ),
-                  #Extension("", ["./storm_analysis/fista/fista_fft.c"], ),
+    extensions = [Extension("storm_analysis.fista._fista_decon_utilities", ["./storm_analysis/fista/fista_decon_utilities.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.fista._fista_fft", ["./storm_analysis/fista/fista_fft.c"],
+                            libraries=library_dirs + ["fftw3"], include_dirs=include_dirs), 
+
                   Extension("storm_analysis.sa_library._matched_filter", ["./storm_analysis/sa_library/matched_filter.c"],
                             libraries=library_dirs + ["fftw3"], include_dirs=include_dirs + []),
                   Extension("storm_analysis.sa_library._grid", ["./storm_analysis/sa_library/grid.c"],
@@ -39,31 +42,63 @@ def get_c_extensions():
                             libraries=library_dirs + ["lapack"], include_dirs=include_dirs + []),
                   Extension("storm_analysis.sa_library._ia_utilities", ["./storm_analysis/sa_library/ia_utilities.c"],
                             libraries=library_dirs, include_dirs=include_dirs),
-                  #Extension("", ["./storm_analysis/dbscan/dbscan.c"], ),
-                  #Extension("", ["./storm_analysis/dbscan/kdtree.c"], ),
-                  #Extension("", ["./storm_analysis/decon_storm/mlem_sparse.c"], ),
-                  #Extension("", ["./storm_analysis/sCMOS/scmos_utilities.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/fista_lib.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_storm.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_sse.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_general.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_common.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_imagea_common.c"], ),
-                  #Extension("", ["./storm_analysis/L1H/homotopy_gpu.c"], ),
-                  #Extension("", ["./storm_analysis/sa_utilities/fitz.c"], ),
-                  #Extension("", ["./storm_analysis/sa_utilities/tracker.c"], ),
-                  #Extension("", ["./storm_analysis/sa_utilities/avemlist.c"], ),
-                  #Extension("", ["./storm_analysis/sa_utilities/apply-drift-correction.c"], ),
-                  #Extension("", ["./storm_analysis/frc/frc.c"], ),
-                  #Extension("", ["./storm_analysis/simulator/draw_gaussians.c"], ),
-                  #Extension("", ["./storm_analysis/simulator/zernike.c"], ),
-                  #Extension("", ["./storm_analysis/spliner/cubic_spline.c"], ),
-                  #Extension("", ["./storm_analysis/spliner/multi_fit_core.c"], ),
-                  #Extension("", ["./storm_analysis/spliner/cubic_fit.c"], ),
-                  #Extension("", ["./storm_analysis/rolling_ball_bgr/rolling_ball_lib.c"], ),
+
+                  Extension("storm_analysis.dbscan._dbscan", ["./storm_analysis/dbscan/dbscan.c",
+                                                              "./storm_analysis/dbscan/kdtree.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),         
+
+                  Extension("storm_analysis.decon_storm._mlem_sparse", ["./storm_analysis/decon_storm/mlem_sparse.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+
+                  Extension("storm_analysis.sCMOS._scmos_utilities", ["./storm_analysis/sCMOS/scmos_utilities.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+  
+                  Extension("storm_analysis.frc._frc", ["./storm_analysis/frc/frc.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+
+                  Extension("storm_analysis.simulator._draw_gaussians", ["./storm_analysis/simulator/draw_gaussians.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.simulator._zernike", ["./storm_analysis/simulator/zernike.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+
+                  Extension("storm_analysis.spliner._cubic_spline", ["./storm_analysis/spliner/cubic_spline.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.spliner._cubic_fit", ["./storm_analysis/spliner/cubic_fit.c",
+                                                                  "./storm_analysis/spliner/multi_fit_core.c",
+                                                                  "./storm_analysis/spliner/cubic_spline.c"],
+                            libraries=library_dirs + ["lapack"], include_dirs=include_dirs),
+
+                  Extension("storm_analysis.rolling_ball_bgr._rolling_ball_lib", ["./storm_analysis/rolling_ball_bgr/rolling_ball_lib.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+
+                  # Executables :
+                  # It's hard to integrate executables into a Python package
+                  # The best way to integrate them would be to convert them into libraries.
+                  # Extension("", ["./storm_analysis/sa_utilities/fitz.c"]),
+                  # Extension("", ["./storm_analysis/sa_utilities/tracker.c"]),
+                  # Extension("", ["./storm_analysis/sa_utilities/avemlist.c"]),
+                  # Extension("", ["./storm_analysis/sa_utilities/apply-drift-correction.c"]),
                   ]
 
+    if platform.system() == 'Windows':
+        extensions += [Extension("storm_analysis.L1H._fista_lib", ["./storm_analysis/L1H/fista_lib.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_storm", ["./storm_analysis/L1H/homotopy_storm.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_sse", ["./storm_analysis/L1H/homotopy_sse.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_general", ["./storm_analysis/L1H/homotopy_general.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_imagea", ["./storm_analysis/L1H/homotopy_imagea.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_common", ["./storm_analysis/L1H/homotopy_common.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_imagea_common", ["./storm_analysis/L1H/homotopy_imagea_common.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       Extension("storm_analysis.L1H._homotopy_gpu", ["./storm_analysis/L1H/homotopy_gpu.c"],
+                                 libraries=library_dirs, include_dirs=include_dirs),
+                       ]
+
     return extensions
 
 setup(
@@ -87,7 +122,7 @@ def get_c_extensions():
         #'hello': ['*.msg'],
     },
     exclude_package_data={
-        #'': ['README.txt']
+        '': ['*README.txt', '*README.md', '*compile*.sh', '*compile*.bat']
     },
     include_package_data=True,
 
diff --git a/storm_analysis/L1H/homotopy_c.py b/storm_analysis/L1H/homotopy_c.py
index fb14c30f..5b9f1f6d 100644
--- a/storm_analysis/L1H/homotopy_c.py
+++ b/storm_analysis/L1H/homotopy_c.py
@@ -21,7 +21,7 @@
 def setCInterface(homotopy_lib):
     global homotopy
 
-    homotopy = loadclib.loadCLibrary(os.path.dirname(__file__), homotopy_lib)
+    homotopy = loadclib.loadCLibrary("storm_analysis.L1H", "_" + homotopy_lib)
 
     l1flt_size = homotopy.getL1FLTSize()
     if(l1flt_size == 4):
diff --git a/storm_analysis/L1H/homotopy_imagea_c.py b/storm_analysis/L1H/homotopy_imagea_c.py
index 1d1ef99c..ce3e0cbd 100644
--- a/storm_analysis/L1H/homotopy_imagea_c.py
+++ b/storm_analysis/L1H/homotopy_imagea_c.py
@@ -22,7 +22,7 @@
 def setCInterface(homotopy_ia_lib):
     global homotopyIa
 
-    homotopyIa = loadclib.loadCLibrary(os.path.dirname(__file__), homotopy_ia_lib)
+    homotopyIa = loadclib.loadCLibrary("storm_analysis.L1H", "_" + homotopy_ia_lib)
 
     # Check that C libraries were compiled as expected.
     l1flt_size = homotopyIa.getL1FLTSize()
diff --git a/storm_analysis/dbscan/dbscan_c.py b/storm_analysis/dbscan/dbscan_c.py
index 870d2c25..69a17bc7 100644
--- a/storm_analysis/dbscan/dbscan_c.py
+++ b/storm_analysis/dbscan/dbscan_c.py
@@ -17,7 +17,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-lib_dbscan = loadclib.loadCLibrary(os.path.dirname(__file__), "dbscan")
+lib_dbscan = loadclib.loadCLibrary("storm_analysis.dbscan", "_dbscan")
 
 lib_dbscan.dbscan.argtypes = [ndpointer(dtype=numpy.float32),
                               ndpointer(dtype=numpy.float32),
@@ -72,7 +72,7 @@ def dbscan(x, y, z, c, eps, min_points, z_factor = 0.5, verbose = True):
     # Print number of clusters
     if verbose:
         n_clusters_ = len(set(c_l)) - (1 if -1 in c_l else 0)
-        print 'Estimated number of clusters: %d' % n_clusters_
+        print('Estimated number of clusters: %d' % n_clusters_)
 
     return c_l
 
diff --git a/storm_analysis/decon_storm/mlem_c.py b/storm_analysis/decon_storm/mlem_c.py
index 8817ce79..36df20b9 100644
--- a/storm_analysis/decon_storm/mlem_c.py
+++ b/storm_analysis/decon_storm/mlem_c.py
@@ -28,7 +28,7 @@
 c_double_p = POINTER(c_double)
 
 # Load mlem C library
-mlem = loadclib.loadCLibrary("mlem_sparse")
+mlem = loadclib.loadCLibrary("storm_analysis.decon_storm", "_mlem_sparse")
 
 # Define structures
 class GAUSS(Structure):
diff --git a/storm_analysis/fista/fista_decon_utilities_c.py b/storm_analysis/fista/fista_decon_utilities_c.py
index 83ac1f19..3c316e53 100644
--- a/storm_analysis/fista/fista_decon_utilities_c.py
+++ b/storm_analysis/fista/fista_decon_utilities_c.py
@@ -13,7 +13,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-fd_util = loadclib.loadCLibrary(os.path.dirname(__file__), "fista_decon_utilities")
+fd_util = loadclib.loadCLibrary("storm_analysis.fista", "_fista_decon_utilities")
 
 # C interface definition
 fd_util.label.argtypes = [ndpointer(dtype=numpy.float64),
diff --git a/storm_analysis/fista/fista_fft_c.py b/storm_analysis/fista/fista_fft_c.py
index 0b2af0bb..caeb4912 100644
--- a/storm_analysis/fista/fista_fft_c.py
+++ b/storm_analysis/fista/fista_fft_c.py
@@ -16,7 +16,7 @@
 
 import storm_analysis.fista.fista_3d as fista3D
 
-fista_fft = loadclib.loadCLibrary(os.path.dirname(__file__), "fista_fft")
+fista_fft = loadclib.loadCLibrary("storm_analysis.fista", "_fista_fft")
 
 # C interface definition
 fista_fft.getXVector.argtypes = [ndpointer(dtype=numpy.float64)]
diff --git a/storm_analysis/frc/frc_c.py b/storm_analysis/frc/frc_c.py
index 54ed88e6..40463ddc 100644
--- a/storm_analysis/frc/frc_c.py
+++ b/storm_analysis/frc/frc_c.py
@@ -13,7 +13,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-frc_lib = loadclib.loadCLibrary(os.path.dirname(__file__), "frc")
+frc_lib = loadclib.loadCLibrary("storm_analysis.frc", "_frc")
 
 # Function specifications.
 frc_lib.calc_frc.argtypes = [ndpointer(dtype=numpy.complex128),
diff --git a/storm_analysis/rolling_ball_bgr/rolling_ball_lib_c.py b/storm_analysis/rolling_ball_bgr/rolling_ball_lib_c.py
index 4db290bb..ade3e8a8 100644
--- a/storm_analysis/rolling_ball_bgr/rolling_ball_lib_c.py
+++ b/storm_analysis/rolling_ball_bgr/rolling_ball_lib_c.py
@@ -18,7 +18,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-rball = loadclib.loadCLibrary(os.path.dirname(__file__), "rolling_ball_lib")
+rball = loadclib.loadCLibrary("storm_analysis.rolling_ball_bgr", "_rolling_ball_lib")
 
 # C interface definition
 rball.estimateBg.argtypes = [ndpointer(dtype=numpy.float64),
diff --git a/storm_analysis/sCMOS/scmos_utilities_c.py b/storm_analysis/sCMOS/scmos_utilities_c.py
index 4c1e4013..9ad2bb1c 100644
--- a/storm_analysis/sCMOS/scmos_utilities_c.py
+++ b/storm_analysis/sCMOS/scmos_utilities_c.py
@@ -18,7 +18,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-slib = loadclib.loadCLibrary(os.path.dirname(__file__), "scmos_utilities")
+slib = loadclib.loadCLibrary("storm_analysis.sCMOS", "_scmos_utilities")
 
 # C interface definition.
 slib.deregularize.argtypes = [ndpointer(dtype=numpy.float64),
diff --git a/storm_analysis/simulator/drawgaussians.py b/storm_analysis/simulator/drawgaussians.py
index 34e18615..5fe00980 100644
--- a/storm_analysis/simulator/drawgaussians.py
+++ b/storm_analysis/simulator/drawgaussians.py
@@ -13,7 +13,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-drawgauss = loadclib.loadCLibrary(os.path.dirname(__file__), "draw_gaussians")
+drawgauss = loadclib.loadCLibrary("storm_analysis.simulator", "_draw_gaussians")
 
 drawgauss.drawGaussians.argtypes = [ndpointer(dtype = numpy.float64),
                                     ndpointer(dtype = numpy.float64),
diff --git a/storm_analysis/simulator/zernike_c.py b/storm_analysis/simulator/zernike_c.py
index a46aee6f..a5c17dfc 100644
--- a/storm_analysis/simulator/zernike_c.py
+++ b/storm_analysis/simulator/zernike_c.py
@@ -13,7 +13,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-zernike = loadclib.loadCLibrary(os.path.dirname(__file__), "zernike")
+zernike = loadclib.loadCLibrary("storm_analysis.simulator", "_zernike")
 
 zernike.zernike.argtypes = [ctypes.c_int,
                             ctypes.c_int,
diff --git a/storm_analysis/spliner/cubic_fit_c.py b/storm_analysis/spliner/cubic_fit_c.py
index f509c3ea..be6c30ad 100644
--- a/storm_analysis/spliner/cubic_fit_c.py
+++ b/storm_analysis/spliner/cubic_fit_c.py
@@ -17,7 +17,7 @@
 import storm_analysis.spliner.spline3D as spline3D
 
 # Load the library.
-cubic_fit = loadclib.loadCLibrary(os.path.dirname(__file__), "cubic_fit")
+cubic_fit = loadclib.loadCLibrary("storm_analysis.spliner", "_cubic_fit")
 
 # C interface definition.
 cubic_fit.fSpline2D.argtypes = [ctypes.c_double,
diff --git a/storm_analysis/spliner/cubic_spline_c.py b/storm_analysis/spliner/cubic_spline_c.py
index b94369c0..57e34a92 100644
--- a/storm_analysis/spliner/cubic_spline_c.py
+++ b/storm_analysis/spliner/cubic_spline_c.py
@@ -13,13 +13,13 @@
 import random
 import sys
 
-import spline2D
-import spline3D
+from storm_analysis.spliner.spline2D import Spline2D
+from storm_analysis.spliner.spline3D import Spline3D
 
 import storm_analysis.sa_library.loadclib as loadclib
 
 # Load the library.
-cubic = loadclib.loadCLibrary(os.path.dirname(__file__), "cubic_spline")
+cubic = loadclib.loadCLibrary("storm_analysis.spliner", "_cubic_spline")
 
 # C interface definition.
 cubic.computeDelta2D.argtypes = [ctypes.c_double,

From bbce626132a52007ee553b70f276c73e659cdd22 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 12:12:03 -0400
Subject: [PATCH 07/17] Add test.py

---
 test.py | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 test.py

diff --git a/test.py b/test.py
new file mode 100644
index 00000000..15531f56
--- /dev/null
+++ b/test.py
@@ -0,0 +1,41 @@
+# Test every extensions have been correctly build
+
+import platform
+
+# Try to import all C extension
+import storm_analysis.sa_library.ia_utilities_c
+import storm_analysis.sa_library.multi_fit_c
+import storm_analysis.sa_library.grid_c
+import storm_analysis.sa_library.matched_filter_c
+
+import storm_analysis.frc.frc_c
+
+import storm_analysis.fista.fista_decon_utilities_c
+import storm_analysis.fista.fista_fft_c
+
+import storm_analysis.fista.fista_fft_c
+
+import storm_analysis.dbscan.dbscan_c
+
+import storm_analysis.decon_storm.mlem_c
+
+import storm_analysis.sCMOS.scmos_utilities_c
+
+import storm_analysis.simulator.zernike_c
+import storm_analysis.simulator.drawgaussians
+
+import storm_analysis.spliner.cubic_spline_c
+import storm_analysis.spliner.cubic_fit_c
+
+import storm_analysis.rolling_ball_bgr.rolling_ball_lib_c
+
+if platform.system() == 'Windows':
+	import storm_analysis.sa_library.loadclib as loadclib
+	loadclib.loadCLibrary("storm_analysis.L1H", "_fista_lib")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_storm")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_sse")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_general")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_imagea")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_common")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_imagea_common")
+	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_gpu")
\ No newline at end of file

From db0f935a0b45cd398c133d84ee31b4bb321ce2ba Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 12:23:56 -0400
Subject: [PATCH 08/17] Add tests

---
 .gitignore                        |  1 +
 setup.py                          |  3 ++
 test.py                           | 41 ---------------------------
 tests/test_c_extensions_import.py | 46 +++++++++++++++++++++++++++++++
 4 files changed, 50 insertions(+), 41 deletions(-)
 delete mode 100644 test.py
 create mode 100644 tests/test_c_extensions_import.py

diff --git a/.gitignore b/.gitignore
index 17aee38f..aef4dc40 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
 *.py[co]
 *.egg-info
 build/
+*.eggs
 
 #############
 ## Emacs
diff --git a/setup.py b/setup.py
index ab948ffe..bf3b9c36 100644
--- a/setup.py
+++ b/setup.py
@@ -127,6 +127,9 @@ def get_c_extensions():
     include_package_data=True,
 
     requires=['numpy (>=1.8.2)', 'setuptools'],
+
+    setup_requires=['pytest-runner'],
+    tests_require=['pytest'],
     
     license="",  
     keywords='storm,microscopy',
diff --git a/test.py b/test.py
deleted file mode 100644
index 15531f56..00000000
--- a/test.py
+++ /dev/null
@@ -1,41 +0,0 @@
-# Test every extensions have been correctly build
-
-import platform
-
-# Try to import all C extension
-import storm_analysis.sa_library.ia_utilities_c
-import storm_analysis.sa_library.multi_fit_c
-import storm_analysis.sa_library.grid_c
-import storm_analysis.sa_library.matched_filter_c
-
-import storm_analysis.frc.frc_c
-
-import storm_analysis.fista.fista_decon_utilities_c
-import storm_analysis.fista.fista_fft_c
-
-import storm_analysis.fista.fista_fft_c
-
-import storm_analysis.dbscan.dbscan_c
-
-import storm_analysis.decon_storm.mlem_c
-
-import storm_analysis.sCMOS.scmos_utilities_c
-
-import storm_analysis.simulator.zernike_c
-import storm_analysis.simulator.drawgaussians
-
-import storm_analysis.spliner.cubic_spline_c
-import storm_analysis.spliner.cubic_fit_c
-
-import storm_analysis.rolling_ball_bgr.rolling_ball_lib_c
-
-if platform.system() == 'Windows':
-	import storm_analysis.sa_library.loadclib as loadclib
-	loadclib.loadCLibrary("storm_analysis.L1H", "_fista_lib")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_storm")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_sse")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_general")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_imagea")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_common")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_imagea_common")
-	loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_gpu")
\ No newline at end of file
diff --git a/tests/test_c_extensions_import.py b/tests/test_c_extensions_import.py
new file mode 100644
index 00000000..48b7c765
--- /dev/null
+++ b/tests/test_c_extensions_import.py
@@ -0,0 +1,46 @@
+# Test every extensions have been correctly build
+
+import platform
+
+def test_c_extensions_import():
+	# Try to import all C extension
+	import storm_analysis.sa_library.ia_utilities_c
+	import storm_analysis.sa_library.multi_fit_c
+	import storm_analysis.sa_library.grid_c
+	import storm_analysis.sa_library.matched_filter_c
+
+	import storm_analysis.frc.frc_c
+
+	import storm_analysis.fista.fista_decon_utilities_c
+	import storm_analysis.fista.fista_fft_c
+
+	import storm_analysis.fista.fista_fft_c
+
+	import storm_analysis.dbscan.dbscan_c
+
+	import storm_analysis.decon_storm.mlem_c
+
+	import storm_analysis.sCMOS.scmos_utilities_c
+
+	import storm_analysis.simulator.zernike_c
+	import storm_analysis.simulator.drawgaussians
+
+	import storm_analysis.spliner.cubic_spline_c
+	import storm_analysis.spliner.cubic_fit_c
+
+	import storm_analysis.rolling_ball_bgr.rolling_ball_lib_c
+
+	if platform.system() == 'Windows':
+		import storm_analysis.sa_library.loadclib as loadclib
+		loadclib.loadCLibrary("storm_analysis.L1H", "_fista_lib")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_storm")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_sse")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_general")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_imagea")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_common")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_imagea_common")
+		loadclib.loadCLibrary("storm_analysis.L1H", "_homotopy_gpu")
+
+
+if __name__ == "__main__":
+	test_c_extensions_import()
\ No newline at end of file

From 9f6f749d3d2c219bec27a64b5d68b394a33e3444 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 13:59:05 -0400
Subject: [PATCH 09/17] Remove setup.py deps

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bf3b9c36..d2a9180b 100644
--- a/setup.py
+++ b/setup.py
@@ -126,7 +126,7 @@ def get_c_extensions():
     },
     include_package_data=True,
 
-    requires=['numpy (>=1.8.2)', 'setuptools'],
+    requires=[],
 
     setup_requires=['pytest-runner'],
     tests_require=['pytest'],

From 28f14471ae0bb3543e11c046e57d459065be9557 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 14:19:26 -0400
Subject: [PATCH 10/17] Add scipy and __init__.py

---
 .gitignore                             | 2 ++
 storm_analysis/decon_storm/__init__.py | 1 +
 2 files changed, 3 insertions(+)
 create mode 100644 storm_analysis/decon_storm/__init__.py

diff --git a/.gitignore b/.gitignore
index aef4dc40..6887c59b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,8 @@
 *.egg-info
 build/
 *.eggs
+dist/
+.cache/
 
 #############
 ## Emacs
diff --git a/storm_analysis/decon_storm/__init__.py b/storm_analysis/decon_storm/__init__.py
new file mode 100644
index 00000000..013e4b7e
--- /dev/null
+++ b/storm_analysis/decon_storm/__init__.py
@@ -0,0 +1 @@
+#!/usr/bin/python

From 2355a6b72d4bd886fc4e8de554c4e9355f66a90d Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 14:34:22 -0400
Subject: [PATCH 11/17] Add setup.cfg

---
 setup.cfg | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 setup.cfg

diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 00000000..9af7e6f1
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,2 @@
+[aliases]
+test=pytest
\ No newline at end of file

From 0cba908971b9c560157bee31608143e7db800244 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Thu, 27 Oct 2016 15:07:06 -0400
Subject: [PATCH 12/17] Move test file

---
 {tests => storm_analysis/tests}/test_c_extensions_import.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {tests => storm_analysis/tests}/test_c_extensions_import.py (100%)

diff --git a/tests/test_c_extensions_import.py b/storm_analysis/tests/test_c_extensions_import.py
similarity index 100%
rename from tests/test_c_extensions_import.py
rename to storm_analysis/tests/test_c_extensions_import.py

From c3e6279213ed2385c8537b0bf55524b831f1ae1d Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Fri, 28 Oct 2016 09:02:34 -0400
Subject: [PATCH 13/17] Add data files

---
 setup.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index d2a9180b..b5634023 100644
--- a/setup.py
+++ b/setup.py
@@ -116,13 +116,15 @@ def get_c_extensions():
     ext_modules=get_c_extensions(),
     package_data={
         #'sample': ['package_data.dat'],
-        # If any package contains *.txt or *.rst files, include them:
-        #'': ['*.txt', '*.rst'],
-        # And include any *.msg files found in the 'hello' package, too:
-        #'hello': ['*.msg'],
+        # README and LICENSE
+        '': ['*.txt', '*.md'],
+        # Matlab files
+        'matlab': ['*.m', '*.mat'],
+        'c_files': ['*.c', '*.h'],
     },
     exclude_package_data={
-        '': ['*README.txt', '*README.md', '*compile*.sh', '*compile*.bat']
+        'scripts': ['*.sh', '*.bat'],
+        'executables': ['*.exe'],
     },
     include_package_data=True,
 

From a87e54824d489ecd53fd091e1c41e32ad424eec1 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Fri, 28 Oct 2016 09:08:51 -0400
Subject: [PATCH 14/17] Integrate sa_utilities extensions

---
 setup.py                                          | 15 ++++++++-------
 .../sa_utilities/apply_drift_correction_c.py      |  2 +-
 storm_analysis/sa_utilities/avemlist_c.py         |  2 +-
 storm_analysis/sa_utilities/fitz_c.py             |  2 +-
 storm_analysis/sa_utilities/tracker_c.py          |  2 +-
 storm_analysis/tests/test_c_extensions_import.py  |  6 ++++++
 6 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/setup.py b/setup.py
index b5634023..266690b3 100644
--- a/setup.py
+++ b/setup.py
@@ -71,13 +71,14 @@ def get_c_extensions():
                   Extension("storm_analysis.rolling_ball_bgr._rolling_ball_lib", ["./storm_analysis/rolling_ball_bgr/rolling_ball_lib.c"],
                             libraries=library_dirs, include_dirs=include_dirs),
 
-                  # Executables :
-                  # It's hard to integrate executables into a Python package
-                  # The best way to integrate them would be to convert them into libraries.
-                  # Extension("", ["./storm_analysis/sa_utilities/fitz.c"]),
-                  # Extension("", ["./storm_analysis/sa_utilities/tracker.c"]),
-                  # Extension("", ["./storm_analysis/sa_utilities/avemlist.c"]),
-                  # Extension("", ["./storm_analysis/sa_utilities/apply-drift-correction.c"]),
+                  Extension("storm_analysis.sa_utilities._fitz", ["./storm_analysis/sa_utilities/fitz.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.sa_utilities._tracker", ["./storm_analysis/sa_utilities/tracker.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.sa_utilities._avemlist", ["./storm_analysis/sa_utilities/avemlist.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.sa_utilities._apply-drift-correction", ["./storm_analysis/sa_utilities/apply-drift-correction.c"],
+                            libraries=library_dirs, include_dirs=include_dirs),
                   ]
 
     if platform.system() == 'Windows':
diff --git a/storm_analysis/sa_utilities/apply_drift_correction_c.py b/storm_analysis/sa_utilities/apply_drift_correction_c.py
index 1e35a3c3..a5acb515 100644
--- a/storm_analysis/sa_utilities/apply_drift_correction_c.py
+++ b/storm_analysis/sa_utilities/apply_drift_correction_c.py
@@ -11,7 +11,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-adc = loadclib.loadCLibrary(os.path.dirname(__file__), "apply-drift-correction")
+adc = loadclib.loadCLibrary("storm_analysis.sa_utilities", "_apply-drift-correction")
 
 adc.applyDriftCorrection.argtypes = [ctypes.c_int,
                                      ctypes.c_void_p]
diff --git a/storm_analysis/sa_utilities/avemlist_c.py b/storm_analysis/sa_utilities/avemlist_c.py
index f1f7e63d..ec5fef1d 100644
--- a/storm_analysis/sa_utilities/avemlist_c.py
+++ b/storm_analysis/sa_utilities/avemlist_c.py
@@ -10,7 +10,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-c_avemlist = loadclib.loadCLibrary(os.path.dirname(__file__), "avemlist")
+c_avemlist = loadclib.loadCLibrary("storm_analysis.sa_utilities", "_avemlist")
 
 c_avemlist.avemlist.argtypes = [ctypes.c_int,
                                 ctypes.c_void_p]
diff --git a/storm_analysis/sa_utilities/fitz_c.py b/storm_analysis/sa_utilities/fitz_c.py
index 36233b67..e8f48032 100644
--- a/storm_analysis/sa_utilities/fitz_c.py
+++ b/storm_analysis/sa_utilities/fitz_c.py
@@ -11,7 +11,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-c_fitz = loadclib.loadCLibrary(os.path.dirname(__file__), "fitz")
+c_fitz = loadclib.loadCLibrary("storm_analysis.sa_utilities", "_fitz")
 
 c_fitz.fitz.argtypes = [ctypes.c_int,
                         ctypes.c_void_p]
diff --git a/storm_analysis/sa_utilities/tracker_c.py b/storm_analysis/sa_utilities/tracker_c.py
index cf3f28f2..dcf9dc1d 100644
--- a/storm_analysis/sa_utilities/tracker_c.py
+++ b/storm_analysis/sa_utilities/tracker_c.py
@@ -11,7 +11,7 @@
 
 import storm_analysis.sa_library.loadclib as loadclib
 
-c_tracker = loadclib.loadCLibrary(os.path.dirname(__file__), "tracker")
+c_tracker = loadclib.loadCLibrary("storm_analysis.sa_utilities", "_tracker")
 
 c_tracker.tracker.argtypes = [ctypes.c_int,
                               ctypes.c_void_p]
diff --git a/storm_analysis/tests/test_c_extensions_import.py b/storm_analysis/tests/test_c_extensions_import.py
index 48b7c765..7052d8fb 100644
--- a/storm_analysis/tests/test_c_extensions_import.py
+++ b/storm_analysis/tests/test_c_extensions_import.py
@@ -4,6 +4,7 @@
 
 def test_c_extensions_import():
 	# Try to import all C extension
+	
 	import storm_analysis.sa_library.ia_utilities_c
 	import storm_analysis.sa_library.multi_fit_c
 	import storm_analysis.sa_library.grid_c
@@ -30,6 +31,11 @@ def test_c_extensions_import():
 
 	import storm_analysis.rolling_ball_bgr.rolling_ball_lib_c
 
+	import storm_analysis.sa_utilities.fitz_c
+	import storm_analysis.sa_utilities.apply_drift_correction_c
+	import storm_analysis.sa_utilities.avemlist_c
+	import storm_analysis.sa_utilities.tracker_c
+
 	if platform.system() == 'Windows':
 		import storm_analysis.sa_library.loadclib as loadclib
 		loadclib.loadCLibrary("storm_analysis.L1H", "_fista_lib")

From 8b3da436ff79973e3326cd8c72c5eed87049e469 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Fri, 28 Oct 2016 09:24:19 -0400
Subject: [PATCH 15/17] Rename test and add MANIFEST.in

---
 MANIFEST.in                                         |  12 ++++++++++++
 setup.py                                            |  12 +++++-------
 storm_analysis/{tests => test/data}/LICENSE.txt     |   0
 storm_analysis/{tests => test/data}/README.txt      |   0
 storm_analysis/{tests => test/data}/calib.npy       | Bin
 storm_analysis/{tests => test/data}/results.txt     |   0
 storm_analysis/{tests => test/data}/test.dax        | Bin
 storm_analysis/{tests => test/data}/test.inf        |   0
 storm_analysis/{tests => test/data}/test_3d_2d.xml  |   0
 .../{tests => test/data}/test_3d_2d_fixed.xml       |   0
 .../data}/test_3d_2d_fixed_low_snr.xml              |   0
 storm_analysis/{tests => test/data}/test_3d_3d.xml  |   0
 storm_analysis/{tests => test/data}/test_3d_Z.xml   |   0
 storm_analysis/{tests => test/data}/test_bg_sub.dax | Bin
 storm_analysis/{tests => test/data}/test_bg_sub.inf |   0
 storm_analysis/{tests => test/data}/test_drift.xml  |   0
 .../{tests => test/data}/test_drift_mlist.bin       | Bin
 storm_analysis/{tests => test/data}/test_l1h.dax    | Bin
 storm_analysis/{tests => test/data}/test_l1h.inf    |   0
 storm_analysis/{tests => test/data}/test_l1h.xml    |   0
 .../{tests => test/data}/test_l1h_olist.bin         | Bin
 .../{tests => test/data}/test_low_snr.dax           | Bin
 .../{tests => test/data}/test_low_snr.inf           |   0
 .../{tests => test/data}/test_low_snr_list.bin      | Bin
 storm_analysis/{tests => test/data}/test_olist.bin  | Bin
 storm_analysis/{tests => test/data}/test_sc_2d.xml  |   0
 .../{tests => test/data}/test_sc_2d_fixed.xml       |   0
 storm_analysis/{tests => test/data}/test_sc_3d.xml  |   0
 storm_analysis/{tests => test/data}/test_sc_Z.xml   |   0
 .../{tests => test/data}/test_spliner.dax           | Bin
 .../{tests => test/data}/test_spliner.inf           |   0
 .../{tests => test/data}/test_spliner_dh.xml        |   0
 .../{tests => test/data}/test_spliner_dh_fista.xml  |   0
 .../{tests => test/data}/test_spliner_olist.bin     | Bin
 storm_analysis/{tests => test}/run_tests.py         |   0
 .../{tests => test}/test_c_extensions_import.py     |   0
 36 files changed, 17 insertions(+), 7 deletions(-)
 create mode 100644 MANIFEST.in
 rename storm_analysis/{tests => test/data}/LICENSE.txt (100%)
 rename storm_analysis/{tests => test/data}/README.txt (100%)
 rename storm_analysis/{tests => test/data}/calib.npy (100%)
 rename storm_analysis/{tests => test/data}/results.txt (100%)
 rename storm_analysis/{tests => test/data}/test.dax (100%)
 rename storm_analysis/{tests => test/data}/test.inf (100%)
 rename storm_analysis/{tests => test/data}/test_3d_2d.xml (100%)
 rename storm_analysis/{tests => test/data}/test_3d_2d_fixed.xml (100%)
 rename storm_analysis/{tests => test/data}/test_3d_2d_fixed_low_snr.xml (100%)
 rename storm_analysis/{tests => test/data}/test_3d_3d.xml (100%)
 rename storm_analysis/{tests => test/data}/test_3d_Z.xml (100%)
 rename storm_analysis/{tests => test/data}/test_bg_sub.dax (100%)
 rename storm_analysis/{tests => test/data}/test_bg_sub.inf (100%)
 rename storm_analysis/{tests => test/data}/test_drift.xml (100%)
 rename storm_analysis/{tests => test/data}/test_drift_mlist.bin (100%)
 rename storm_analysis/{tests => test/data}/test_l1h.dax (100%)
 rename storm_analysis/{tests => test/data}/test_l1h.inf (100%)
 rename storm_analysis/{tests => test/data}/test_l1h.xml (100%)
 rename storm_analysis/{tests => test/data}/test_l1h_olist.bin (100%)
 rename storm_analysis/{tests => test/data}/test_low_snr.dax (100%)
 rename storm_analysis/{tests => test/data}/test_low_snr.inf (100%)
 rename storm_analysis/{tests => test/data}/test_low_snr_list.bin (100%)
 rename storm_analysis/{tests => test/data}/test_olist.bin (100%)
 rename storm_analysis/{tests => test/data}/test_sc_2d.xml (100%)
 rename storm_analysis/{tests => test/data}/test_sc_2d_fixed.xml (100%)
 rename storm_analysis/{tests => test/data}/test_sc_3d.xml (100%)
 rename storm_analysis/{tests => test/data}/test_sc_Z.xml (100%)
 rename storm_analysis/{tests => test/data}/test_spliner.dax (100%)
 rename storm_analysis/{tests => test/data}/test_spliner.inf (100%)
 rename storm_analysis/{tests => test/data}/test_spliner_dh.xml (100%)
 rename storm_analysis/{tests => test/data}/test_spliner_dh_fista.xml (100%)
 rename storm_analysis/{tests => test/data}/test_spliner_olist.bin (100%)
 rename storm_analysis/{tests => test}/run_tests.py (100%)
 rename storm_analysis/{tests => test}/test_c_extensions_import.py (100%)

diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 00000000..9cd28b59
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,12 @@
+recursive-include storm_analysis *.py
+recursive-include storm_analysis *.ui
+recursive-include storm_analysis *.txt
+recursive-include storm_analysis *.md
+recursive-include storm_analysis *.m
+recursive-include storm_analysis *.mat
+recursive-include storm_analysis *.c
+recursive-include storm_analysis *.h
+recursive-include storm_analysis */data/*
+recursive-include storm_analysis */sample_data/*
+recursive-include storm_analysis *tests*
+
diff --git a/setup.py b/setup.py
index 266690b3..b7438188 100644
--- a/setup.py
+++ b/setup.py
@@ -116,16 +116,14 @@ def get_c_extensions():
 
     ext_modules=get_c_extensions(),
     package_data={
-        #'sample': ['package_data.dat'],
-        # README and LICENSE
         '': ['*.txt', '*.md'],
-        # Matlab files
-        'matlab': ['*.m', '*.mat'],
-        'c_files': ['*.c', '*.h'],
+
+        '': ['*.m', '*.mat'],
+        '': ['*.c', '*.h'],
+        '': ['*tests*'],
+        '': ['*data*'],
     },
     exclude_package_data={
-        'scripts': ['*.sh', '*.bat'],
-        'executables': ['*.exe'],
     },
     include_package_data=True,
 
diff --git a/storm_analysis/tests/LICENSE.txt b/storm_analysis/test/data/LICENSE.txt
similarity index 100%
rename from storm_analysis/tests/LICENSE.txt
rename to storm_analysis/test/data/LICENSE.txt
diff --git a/storm_analysis/tests/README.txt b/storm_analysis/test/data/README.txt
similarity index 100%
rename from storm_analysis/tests/README.txt
rename to storm_analysis/test/data/README.txt
diff --git a/storm_analysis/tests/calib.npy b/storm_analysis/test/data/calib.npy
similarity index 100%
rename from storm_analysis/tests/calib.npy
rename to storm_analysis/test/data/calib.npy
diff --git a/storm_analysis/tests/results.txt b/storm_analysis/test/data/results.txt
similarity index 100%
rename from storm_analysis/tests/results.txt
rename to storm_analysis/test/data/results.txt
diff --git a/storm_analysis/tests/test.dax b/storm_analysis/test/data/test.dax
similarity index 100%
rename from storm_analysis/tests/test.dax
rename to storm_analysis/test/data/test.dax
diff --git a/storm_analysis/tests/test.inf b/storm_analysis/test/data/test.inf
similarity index 100%
rename from storm_analysis/tests/test.inf
rename to storm_analysis/test/data/test.inf
diff --git a/storm_analysis/tests/test_3d_2d.xml b/storm_analysis/test/data/test_3d_2d.xml
similarity index 100%
rename from storm_analysis/tests/test_3d_2d.xml
rename to storm_analysis/test/data/test_3d_2d.xml
diff --git a/storm_analysis/tests/test_3d_2d_fixed.xml b/storm_analysis/test/data/test_3d_2d_fixed.xml
similarity index 100%
rename from storm_analysis/tests/test_3d_2d_fixed.xml
rename to storm_analysis/test/data/test_3d_2d_fixed.xml
diff --git a/storm_analysis/tests/test_3d_2d_fixed_low_snr.xml b/storm_analysis/test/data/test_3d_2d_fixed_low_snr.xml
similarity index 100%
rename from storm_analysis/tests/test_3d_2d_fixed_low_snr.xml
rename to storm_analysis/test/data/test_3d_2d_fixed_low_snr.xml
diff --git a/storm_analysis/tests/test_3d_3d.xml b/storm_analysis/test/data/test_3d_3d.xml
similarity index 100%
rename from storm_analysis/tests/test_3d_3d.xml
rename to storm_analysis/test/data/test_3d_3d.xml
diff --git a/storm_analysis/tests/test_3d_Z.xml b/storm_analysis/test/data/test_3d_Z.xml
similarity index 100%
rename from storm_analysis/tests/test_3d_Z.xml
rename to storm_analysis/test/data/test_3d_Z.xml
diff --git a/storm_analysis/tests/test_bg_sub.dax b/storm_analysis/test/data/test_bg_sub.dax
similarity index 100%
rename from storm_analysis/tests/test_bg_sub.dax
rename to storm_analysis/test/data/test_bg_sub.dax
diff --git a/storm_analysis/tests/test_bg_sub.inf b/storm_analysis/test/data/test_bg_sub.inf
similarity index 100%
rename from storm_analysis/tests/test_bg_sub.inf
rename to storm_analysis/test/data/test_bg_sub.inf
diff --git a/storm_analysis/tests/test_drift.xml b/storm_analysis/test/data/test_drift.xml
similarity index 100%
rename from storm_analysis/tests/test_drift.xml
rename to storm_analysis/test/data/test_drift.xml
diff --git a/storm_analysis/tests/test_drift_mlist.bin b/storm_analysis/test/data/test_drift_mlist.bin
similarity index 100%
rename from storm_analysis/tests/test_drift_mlist.bin
rename to storm_analysis/test/data/test_drift_mlist.bin
diff --git a/storm_analysis/tests/test_l1h.dax b/storm_analysis/test/data/test_l1h.dax
similarity index 100%
rename from storm_analysis/tests/test_l1h.dax
rename to storm_analysis/test/data/test_l1h.dax
diff --git a/storm_analysis/tests/test_l1h.inf b/storm_analysis/test/data/test_l1h.inf
similarity index 100%
rename from storm_analysis/tests/test_l1h.inf
rename to storm_analysis/test/data/test_l1h.inf
diff --git a/storm_analysis/tests/test_l1h.xml b/storm_analysis/test/data/test_l1h.xml
similarity index 100%
rename from storm_analysis/tests/test_l1h.xml
rename to storm_analysis/test/data/test_l1h.xml
diff --git a/storm_analysis/tests/test_l1h_olist.bin b/storm_analysis/test/data/test_l1h_olist.bin
similarity index 100%
rename from storm_analysis/tests/test_l1h_olist.bin
rename to storm_analysis/test/data/test_l1h_olist.bin
diff --git a/storm_analysis/tests/test_low_snr.dax b/storm_analysis/test/data/test_low_snr.dax
similarity index 100%
rename from storm_analysis/tests/test_low_snr.dax
rename to storm_analysis/test/data/test_low_snr.dax
diff --git a/storm_analysis/tests/test_low_snr.inf b/storm_analysis/test/data/test_low_snr.inf
similarity index 100%
rename from storm_analysis/tests/test_low_snr.inf
rename to storm_analysis/test/data/test_low_snr.inf
diff --git a/storm_analysis/tests/test_low_snr_list.bin b/storm_analysis/test/data/test_low_snr_list.bin
similarity index 100%
rename from storm_analysis/tests/test_low_snr_list.bin
rename to storm_analysis/test/data/test_low_snr_list.bin
diff --git a/storm_analysis/tests/test_olist.bin b/storm_analysis/test/data/test_olist.bin
similarity index 100%
rename from storm_analysis/tests/test_olist.bin
rename to storm_analysis/test/data/test_olist.bin
diff --git a/storm_analysis/tests/test_sc_2d.xml b/storm_analysis/test/data/test_sc_2d.xml
similarity index 100%
rename from storm_analysis/tests/test_sc_2d.xml
rename to storm_analysis/test/data/test_sc_2d.xml
diff --git a/storm_analysis/tests/test_sc_2d_fixed.xml b/storm_analysis/test/data/test_sc_2d_fixed.xml
similarity index 100%
rename from storm_analysis/tests/test_sc_2d_fixed.xml
rename to storm_analysis/test/data/test_sc_2d_fixed.xml
diff --git a/storm_analysis/tests/test_sc_3d.xml b/storm_analysis/test/data/test_sc_3d.xml
similarity index 100%
rename from storm_analysis/tests/test_sc_3d.xml
rename to storm_analysis/test/data/test_sc_3d.xml
diff --git a/storm_analysis/tests/test_sc_Z.xml b/storm_analysis/test/data/test_sc_Z.xml
similarity index 100%
rename from storm_analysis/tests/test_sc_Z.xml
rename to storm_analysis/test/data/test_sc_Z.xml
diff --git a/storm_analysis/tests/test_spliner.dax b/storm_analysis/test/data/test_spliner.dax
similarity index 100%
rename from storm_analysis/tests/test_spliner.dax
rename to storm_analysis/test/data/test_spliner.dax
diff --git a/storm_analysis/tests/test_spliner.inf b/storm_analysis/test/data/test_spliner.inf
similarity index 100%
rename from storm_analysis/tests/test_spliner.inf
rename to storm_analysis/test/data/test_spliner.inf
diff --git a/storm_analysis/tests/test_spliner_dh.xml b/storm_analysis/test/data/test_spliner_dh.xml
similarity index 100%
rename from storm_analysis/tests/test_spliner_dh.xml
rename to storm_analysis/test/data/test_spliner_dh.xml
diff --git a/storm_analysis/tests/test_spliner_dh_fista.xml b/storm_analysis/test/data/test_spliner_dh_fista.xml
similarity index 100%
rename from storm_analysis/tests/test_spliner_dh_fista.xml
rename to storm_analysis/test/data/test_spliner_dh_fista.xml
diff --git a/storm_analysis/tests/test_spliner_olist.bin b/storm_analysis/test/data/test_spliner_olist.bin
similarity index 100%
rename from storm_analysis/tests/test_spliner_olist.bin
rename to storm_analysis/test/data/test_spliner_olist.bin
diff --git a/storm_analysis/tests/run_tests.py b/storm_analysis/test/run_tests.py
similarity index 100%
rename from storm_analysis/tests/run_tests.py
rename to storm_analysis/test/run_tests.py
diff --git a/storm_analysis/tests/test_c_extensions_import.py b/storm_analysis/test/test_c_extensions_import.py
similarity index 100%
rename from storm_analysis/tests/test_c_extensions_import.py
rename to storm_analysis/test/test_c_extensions_import.py

From cd150219060679b7f58612e4b53933701d51a2e7 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Fri, 28 Oct 2016 09:29:22 -0400
Subject: [PATCH 16/17] Tweak setup.py

---
 setup.py | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/setup.py b/setup.py
index b7438188..2a7fbb72 100644
--- a/setup.py
+++ b/setup.py
@@ -115,16 +115,8 @@ def get_c_extensions():
     packages=find_packages(),
 
     ext_modules=get_c_extensions(),
-    package_data={
-        '': ['*.txt', '*.md'],
-
-        '': ['*.m', '*.mat'],
-        '': ['*.c', '*.h'],
-        '': ['*tests*'],
-        '': ['*data*'],
-    },
-    exclude_package_data={
-    },
+    package_data={},
+    exclude_package_data={},
     include_package_data=True,
 
     requires=[],

From 50d480192a2171c55da788ba24e4d29431cc1cd6 Mon Sep 17 00:00:00 2001
From: Hadrien Mary <hadrien.mary@gmail.com>
Date: Fri, 28 Oct 2016 10:20:11 -0400
Subject: [PATCH 17/17] More tests

---
 .gitignore                                    |   1 +
 MANIFEST.in                                   |   2 +
 storm_analysis/__init__.py                    |  23 ++
 storm_analysis/frc/frc_calc2d.py              | 168 +++++----
 storm_analysis/rcc/rcc-drift-correction.py    | 329 -----------------
 storm_analysis/rcc/rcc_drift_correction.py    | 338 ++++++++++++++++++
 storm_analysis/test/run_tests.py              |  17 +-
 .../test/test_c_extensions_import.py          |   2 +-
 storm_analysis/test/test_frc.py               |  14 +
 storm_analysis/test/test_rcc.py               |  14 +
 10 files changed, 496 insertions(+), 412 deletions(-)
 delete mode 100644 storm_analysis/rcc/rcc-drift-correction.py
 create mode 100644 storm_analysis/rcc/rcc_drift_correction.py
 create mode 100644 storm_analysis/test/test_frc.py
 create mode 100644 storm_analysis/test/test_rcc.py

diff --git a/.gitignore b/.gitignore
index 6887c59b..2fc01b86 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,6 +8,7 @@ build/
 *.eggs
 dist/
 .cache/
+storm_analysis/test/output/
 
 #############
 ## Emacs
diff --git a/MANIFEST.in b/MANIFEST.in
index 9cd28b59..da9d6761 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -10,3 +10,5 @@ recursive-include storm_analysis */data/*
 recursive-include storm_analysis */sample_data/*
 recursive-include storm_analysis *tests*
 
+prune storm_analysis/test/output
+
diff --git a/storm_analysis/__init__.py b/storm_analysis/__init__.py
index 013e4b7e..1c4152d6 100644
--- a/storm_analysis/__init__.py
+++ b/storm_analysis/__init__.py
@@ -1 +1,24 @@
 #!/usr/bin/python
+import os
+
+
+def get_data(data_path):
+    import pkg_resources
+    data = pkg_resources.resource_filename(__name__, data_path)
+    return data
+
+
+def get_path(path):
+    return os.path.join(os.path.dirname(os.path.abspath(__file__)), path)
+
+
+def get_path_output_test(fname=None):
+    out_path = get_path("test/output/")
+    
+    if not os.path.exists(out_path):
+        os.makedirs(out_path)
+    
+    if fname:
+        return os.path.join(out_path, fname)
+    else:
+        return out_path
\ No newline at end of file
diff --git a/storm_analysis/frc/frc_calc2d.py b/storm_analysis/frc/frc_calc2d.py
index 3a892af2..b2c6116d 100644
--- a/storm_analysis/frc/frc_calc2d.py
+++ b/storm_analysis/frc/frc_calc2d.py
@@ -12,91 +12,103 @@
 import matplotlib.pyplot as pyplot
 import numpy
 import sys
+import argparse
 
 import storm_analysis.frc.frc_c as frcC
 import storm_analysis.sa_library.arraytoimage as arraytoimage
 import storm_analysis.sa_library.i3togrid as i3togrid
 import storm_analysis.sa_library.readinsight3 as readinsight3
 
-pixel_size = 160.0
-storm_scale = 8
-
-if (len(sys.argv) < 3):
-    print("usage: <in_list.bin> <results.txt> <show plot 0,1 (optional)>")
-    exit()
-
-# Load the data.
-i3_grid = i3togrid.I3GData(sys.argv[1], scale = storm_scale)
-
-# Split the data (approximately) in half & generate 2D histograms.
-print("Searching for mid-point")
-
-# For simulations the .dax file might not actually have as many 
-# frames as the molecule list so use a hack to get the number of
-# frames in the molecule list.
-max_f = int(numpy.max(i3_grid.i3data['fr'])) + 1
-locs = round(numpy.sum(i3_grid.i3To2DGridAllChannelsMerged(fmax = max_f)))
-
-start = 0
-end = max_f
-half_locs = locs/2
-while ((end - start) > 1):
-    mid = (end - start)/2 + start
-    print("  ", start, mid, end)
-    grid1 = i3_grid.i3To2DGridAllChannelsMerged(fmin = 0, fmax = mid)
-    if (numpy.sum(grid1) < half_locs):
-        start = mid
-    else:
-        end = mid
-
-print(" mid-point:", end)
-grid1 = i3_grid.i3To2DGridAllChannelsMerged(fmin = 0, fmax = end)
-grid2 = i3_grid.i3To2DGridAllChannelsMerged(fmin = end, fmax = max_f)
-
-# Compute FFT
-print("Calculating")
-grid1_fft = numpy.fft.fftshift(numpy.fft.fft2(grid1))
-grid2_fft = numpy.fft.fftshift(numpy.fft.fft2(grid2))
-
-grid1_fft_sqr = grid1_fft * numpy.conj(grid1_fft)
-grid2_fft_sqr = grid2_fft * numpy.conj(grid2_fft)
-grid1_grid2 = grid1_fft * numpy.conj(grid2_fft)
-
-if 1:
-    arraytoimage.singleColorImage(numpy.abs(grid1_fft), "grid1")
-    arraytoimage.singleColorImage(numpy.abs(grid2_fft), "grid2")
-
-[frc, frc_counts] = frcC.frc(grid1_fft, grid2_fft)
-
-# Plot results
-for i in range(frc.size):
-    if (frc_counts[i] > 0):
-        frc[i] = frc[i]/float(frc_counts[i])
-    else:
-        frc[i] = 0.0
-
-xvals = numpy.arange(frc.size)
-xvals = xvals/(float(grid1_fft.shape[0]) * pixel_size * (1.0/float(storm_scale)))
-frc = numpy.real(frc)
-
-fp = open(sys.argv[2], "w")
-for i in range(xvals.size):
-    fp.write(str(xvals[i]) + "," + str(frc[i]) + "\n")
-fp.close()
-
-if (len(sys.argv) == 4) and (sys.argv[3] == "0"):
-    exit()
-        
-fig = pyplot.figure()
-ax = fig.add_subplot(111)
-ax.scatter(xvals, frc)
-pyplot.xlim([xvals[0], xvals[-1]])
-pyplot.ylim([-0.2,1.2])
-pyplot.xlabel("Spatial Frequency (nm-1)")
-pyplot.ylabel("Correlation")
-pyplot.show()
 
-#
+def calc2d(in_list, results, show_plot):
+
+    pixel_size = 160.0
+    storm_scale = 8
+
+    # Load the data.
+    i3_grid = i3togrid.I3GData(in_list, scale = storm_scale)
+
+    # Split the data (approximately) in half & generate 2D histograms.
+    print("Searching for mid-point")
+
+    # For simulations the .dax file might not actually have as many 
+    # frames as the molecule list so use a hack to get the number of
+    # frames in the molecule list.
+    max_f = int(numpy.max(i3_grid.i3data['fr'])) + 1
+    locs = round(numpy.sum(i3_grid.i3To2DGridAllChannelsMerged(fmax = max_f)))
+
+    start = 0
+    end = max_f
+    half_locs = locs/2
+    while ((end - start) > 1):
+        mid = (end - start)/2 + start
+        print("  ", start, mid, end)
+        grid1 = i3_grid.i3To2DGridAllChannelsMerged(fmin = 0, fmax = mid)
+        if (numpy.sum(grid1) < half_locs):
+            start = mid
+        else:
+            end = mid
+
+    print(" mid-point:", end)
+    grid1 = i3_grid.i3To2DGridAllChannelsMerged(fmin = 0, fmax = end)
+    grid2 = i3_grid.i3To2DGridAllChannelsMerged(fmin = end, fmax = max_f)
+
+    # Compute FFT
+    print("Calculating")
+    grid1_fft = numpy.fft.fftshift(numpy.fft.fft2(grid1))
+    grid2_fft = numpy.fft.fftshift(numpy.fft.fft2(grid2))
+
+    grid1_fft_sqr = grid1_fft * numpy.conj(grid1_fft)
+    grid2_fft_sqr = grid2_fft * numpy.conj(grid2_fft)
+    grid1_grid2 = grid1_fft * numpy.conj(grid2_fft)
+
+    if show_plot:
+        arraytoimage.singleColorImage(numpy.abs(grid1_fft), "grid1")
+        arraytoimage.singleColorImage(numpy.abs(grid2_fft), "grid2")
+
+    [frc, frc_counts] = frcC.frc(grid1_fft, grid2_fft)
+
+    # Plot results
+    for i in range(frc.size):
+        if (frc_counts[i] > 0):
+            frc[i] = frc[i]/float(frc_counts[i])
+        else:
+            frc[i] = 0.0
+
+    xvals = numpy.arange(frc.size)
+    xvals = xvals/(float(grid1_fft.shape[0]) * pixel_size * (1.0/float(storm_scale)))
+    frc = numpy.real(frc)
+
+    fp = open(results, "w")
+    for i in range(xvals.size):
+        fp.write(str(xvals[i]) + "," + str(frc[i]) + "\n")
+    fp.close()
+
+    if show_plot:
+            
+        fig = pyplot.figure()
+        ax = fig.add_subplot(111)
+        ax.scatter(xvals, frc)
+        pyplot.xlim([xvals[0], xvals[-1]])
+        pyplot.ylim([-0.2,1.2])
+        pyplot.xlabel("Spatial Frequency (nm-1)")
+        pyplot.ylabel("Correlation")
+        pyplot.show()
+
+
+if __name__ == "__main__":
+
+
+    parser = argparse.ArgumentParser(description='Calculate 2D FRC following Nieuwenhuizen, Nature Methods, 2013')
+    
+    parser.add_argument('--in', dest='in_list', type=str, required=True)
+    parser.add_argument('--res', dest='results', type=str, required=True)
+    parser.add_argument('--plot', dest='show_plot', type=bool, required=False, default=False)
+
+    args = parser.parse_args()
+
+    calc2d(args.in_list, args.results, args.show_plot)
+
 # The MIT License
 #
 # Copyright (c) 2014 Zhuang Lab, Harvard University
diff --git a/storm_analysis/rcc/rcc-drift-correction.py b/storm_analysis/rcc/rcc-drift-correction.py
deleted file mode 100644
index 9c3eac44..00000000
--- a/storm_analysis/rcc/rcc-drift-correction.py
+++ /dev/null
@@ -1,329 +0,0 @@
-#!/usr/bin/python
-#
-# A Python implementation of the drift algorithm described in this reference:
-#
-# "Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm", 
-# Wang et al. Optics Express, 30 June 2014, Vol. 22, No. 13, DOI:10.1364/OE.22.015982.
-#
-# This uses the above algorithm for XY correction, then falls back to old
-# approach for the Z correction.
-#
-# Hazen 09/14
-#
-
-import numpy
-import os
-import pickle
-import scipy.interpolate
-import scipy.signal
-import sys
-
-import storm_analysis.sa_library.arraytoimage as arraytoimage
-import storm_analysis.sa_library.driftutilities as driftutilities
-import storm_analysis.sa_library.i3togrid as i3togrid
-import storm_analysis.sa_library.imagecorrelation as imagecorrelation
-
-
-# Setup
-if (len(sys.argv) < 5):
-    print("usage: <bin> <drift.txt> <step> <scale> <optional - z_correct>")
-    exit()
-
-step = int(sys.argv[3])
-scale = int(sys.argv[4])
-i3_data = i3togrid.I3GDataLL(sys.argv[1], scale = scale)
-film_l = i3_data.getFilmLength()
-max_err = 0.2
-
-correct_z = True
-if (len(sys.argv) > 5):
-    correct_z = False
-
-# Sub-routines.
-def saveDriftData(fdx, fdy, fdz):
-    driftutilities.saveDriftData(sys.argv[2], fdx, fdy, fdz)
-
-def interpolateData(xvals, yvals):
-    return driftutilities.interpolateData(xvals, yvals, film_l)
-
-# Don't analyze films that are too short.
-if (4 * step > film_l):
-    saveDriftData(numpy.zeros(film_l),
-                  numpy.zeros(film_l),
-                  numpy.zeros(film_l))
-    exit()
-
-print("Performing XY correction.")
-
-# Compute offsets between all pairs of sub images.
-endpost = film_l - step/2
-old_start1 = -1
-start1 = 0
-end1 = start1 + step
-start2 = start1
-end2 = start2 + step
-i = 0
-j = 0
-centers = [(end1 - start1)/2 + start1]
-pairs = []
-while (start1 < endpost):
-
-    if (start2 > endpost):
-        i += 1
-        j = i
-        start1 += step
-        end1 = start1 + step
-        start2 = start1
-        end2 = start2 + step
-        if (end1 > endpost):
-            end1 = film_l
-        if (end2 > endpost):
-            end2 = film_l
-        if (start1 < endpost):
-            centers.append((end1 - start1)/2 + start1)
-
-    if (start1 > endpost):
-        continue
-
-    if not (start1 == start2):
-        if (old_start1 != start1):
-            i3_data.loadDataInFrames(fmin = start1, fmax = end1-1)
-            sub1 = i3_data.i3To2DGridAllChannelsMerged(uncorrected = True)
-            old_start1 = start1
-
-        i3_data.loadDataInFrames(fmin = start2, fmax = end2-1)
-        sub2 = i3_data.i3To2DGridAllChannelsMerged(uncorrected = True)
-
-        [corr, dx, dy, success] = imagecorrelation.xyOffset(sub1,
-                                                            sub2,
-                                                            scale)
-
-        dx = dx/float(scale)
-        dy = dy/float(scale)
-
-        print("offset between frame ranges ", start1, "-" , end1 , " and ", start2, "-", end2)
-
-        if success:
-            print(" -> ", dx, dy, "good")
-        else:
-            print(" -> ", dx, dy, "bad")
-        print("")
-
-        pairs.append([i, j, dx, dy, success])
-
-    j += 1
-    start2 += step
-    end2 = start2 + step
-    if (end2 > endpost):
-        end2 = film_l
-
-
-print("--")
-
-#
-# For testing it is faster to not have to re-run the
-# XY drift correction calculations.
-#
-#with open("test.dat", "w") as fp:
-#    pickle.dump([centers, pairs], fp)
-#
-#with open("test.dat") as fp:
-#    [centers, pairs] = pickle.load(fp)
-#
-
-# Prepare rij_x, rij_y, A matrix.
-rij_x = numpy.zeros(len(pairs), dtype = numpy.float32)
-rij_y = numpy.zeros(len(pairs), dtype = numpy.float32)
-A = numpy.zeros((len(pairs),len(centers)), dtype = numpy.float32)
-for i, pair in enumerate(pairs):
-    rij_x[i] = pair[2]
-    rij_y[i] = pair[3]
-    A[i,pair[0]:pair[1]] = 1.0
-
-# Calculate drift (pass1). 
-# dx and dy contain the optimal offset between sub image i and sub image i+1 in x/y.
-pinv_A = numpy.linalg.pinv(A)
-dx = numpy.dot(pinv_A, rij_x)
-dy = numpy.dot(pinv_A, rij_y)
-
-# Calculate errors.
-err_x = numpy.dot(A, dx) - rij_x
-err_y = numpy.dot(A, dy) - rij_y
-
-err_d = numpy.sqrt(err_x * err_x + err_y * err_y)
-arg_sort_err = numpy.argsort(err_d)
-
-# Print errors before.
-if 0:
-    print("Before:")
-    for i in range(err_d.size):
-        print(i, rij_x[i], rij_y[i], A[i,:], err_d[i])
-    print("")
-
-# Remove bad values.
-j = len(arg_sort_err) - 1
-
-while (j > 0) and (err_d[arg_sort_err[j]] > max_err):
-    index = arg_sort_err[j]
-    delA = numpy.delete(A, index, 0)
-    if (numpy.linalg.matrix_rank(delA, tol = 1.0) == (len(centers)-1)):
-        print(j, "removing", index, "with error", err_d[index])
-        A = delA
-        rij_x = numpy.delete(rij_x, index, 0)
-        rij_y = numpy.delete(rij_y, index, 0)
-        err_d = numpy.delete(err_d, index, 0)
-        arg_sort_err[(arg_sort_err > index)] -= 1
-    else:
-        print("not removing", index, "with error", err_d[index])
-    j -= 1
-
-# Print errors after.
-if 0:
-    print("")
-    print("After:")
-    for i in range(err_d.size):
-        print(i, rij_x[i], rij_y[i], A[i,:], err_d[i])
-    print("")
-
-# Calculate drift (pass2). 
-pinv_A = numpy.linalg.pinv(A)
-dx = numpy.dot(pinv_A, rij_x)
-dy = numpy.dot(pinv_A, rij_y)
-
-
-# Integrate to get final drift.
-driftx = numpy.zeros((dx.size))
-drifty = numpy.zeros((dy.size))
-for i in range(dx.size):
-    driftx[i] = numpy.sum(dx[0:i])
-    drifty[i] = numpy.sum(dy[0:i])
-
-if 1:
-    for i in range(driftx.size):
-        print(i, centers[i], driftx[i], drifty[i])
-
-# Create spline for interpolation.
-final_driftx = interpolateData(centers, driftx)
-final_drifty = interpolateData(centers, drifty)
-
-# Plot XY drift.
-if 0:
-    import matplotlib
-    import matplotlib.pyplot as pyplot
-
-    x = numpy.arange(film_l)
-    fig = pyplot.figure()
-    ax = fig.add_subplot(111)
-    ax.plot(x, final_driftx, color = 'blue')
-    ax.plot(x, final_drifty, color = 'red')
-    pyplot.show()
-
-# Z correction.
-if not correct_z:
-    saveDriftData(final_driftx,
-                  final_drifty,
-                  numpy.zeros(film_l))
-    exit()
-
-print("")
-print("Performing Z Correction.")
-
-start = 0
-z_bins = 20
-i3_data.loadDataInFrames(fmin = start, fmax = start+step)
-
-if correct_z:
-    z_bins = 20
-    xyzmaster = i3_data.i3To3DGridAllChannelsMerged(z_bins,
-                                                    uncorrected = True)
-
-j = 0
-index = 0
-old_dz = 0.0
-driftz = numpy.zeros((dx.size))
-while(j < film_l):
-
-    # Load correct frame range.
-    if ((j + 2*step) >= film_l):
-        i3_data.loadDataInFrames(fmin = j)
-        step_step = 2*step
-    else:
-        i3_data.loadDataInFrames(fmin = j, fmax = j + step)
-        step_step = step
-
-    # Apply XY drift correction.
-    i3_data.applyXYDriftCorrection(driftx[index], drifty[index])
-
-    # Z correlation
-    dz = old_dz
-
-    xyzcurr = i3_data.i3To3DGridAllChannelsMerged(z_bins,
-                                                  uncorrected = True)
-
-    [corr, fit, dz, z_success] = imagecorrelation.zOffset(xyzmaster, xyzcurr)
-
-    # Update Values
-    if z_success:
-        old_dz = dz
-    else:
-        dz = old_dz
-            
-    dz = dz * 1000.0/float(z_bins)
-    
-    if z_success:
-        i3_data.applyZDriftCorrection(-dz)
-        xyzmaster += i3_data.i3To3DGridAllChannelsMerged(z_bins)
-
-    driftz[index] = dz
-
-    if z_success:
-        print(index, dz, "good")
-    else:
-        print(index, dz, "bad")
-
-    index += 1
-    j += step_step
-
-final_driftz = interpolateData(centers, driftz)
-
-saveDriftData(final_driftx,
-              final_drifty,
-              final_driftz)
-
-# Plot X,Y, Z drift.
-if False:
-    import matplotlib
-    import matplotlib.pyplot as pyplot
-
-    pixel_size = 160.0 # pixel size in nm.
-    x = numpy.arange(film_l)
-    fig = pyplot.figure()
-    ax = fig.add_subplot(111)
-    ax.plot(x, pixel_size * final_driftx, color = 'red')
-    ax.plot(x, pixel_size * final_drifty, color = 'green')
-    ax.plot(x, final_driftz, color = 'blue')
-    pyplot.show()
-
-#
-# The MIT License
-#
-# Copyright (c) 2014 Zhuang Lab, Harvard University
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
diff --git a/storm_analysis/rcc/rcc_drift_correction.py b/storm_analysis/rcc/rcc_drift_correction.py
new file mode 100644
index 00000000..32b7c412
--- /dev/null
+++ b/storm_analysis/rcc/rcc_drift_correction.py
@@ -0,0 +1,338 @@
+#!/usr/bin/python
+#
+# A Python implementation of the drift algorithm described in this reference:
+#
+# "Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm", 
+# Wang et al. Optics Express, 30 June 2014, Vol. 22, No. 13, DOI:10.1364/OE.22.015982.
+#
+# This uses the above algorithm for XY correction, then falls back to old
+# approach for the Z correction.
+#
+# Hazen 09/14
+#
+
+import numpy
+import os
+import pickle
+import scipy.interpolate
+import scipy.signal
+import sys
+import argparse
+
+import storm_analysis.sa_library.arraytoimage as arraytoimage
+import storm_analysis.sa_library.driftutilities as driftutilities
+import storm_analysis.sa_library.i3togrid as i3togrid
+import storm_analysis.sa_library.imagecorrelation as imagecorrelation
+
+
+def rcc(bin, drift, step, scale, correct_z=True, show_plot=False):
+
+    i3_data = i3togrid.I3GDataLL(bin, scale = scale)
+    film_l = i3_data.getFilmLength()
+    max_err = 0.2
+
+    # Sub-routines.
+    def saveDriftData(fdx, fdy, fdz):
+        driftutilities.saveDriftData(drift, fdx, fdy, fdz)
+
+    def interpolateData(xvals, yvals):
+        return driftutilities.interpolateData(xvals, yvals, film_l)
+
+    # Don't analyze films that are too short.
+    if (4 * step > film_l):
+        saveDriftData(numpy.zeros(film_l),
+                      numpy.zeros(film_l),
+                      numpy.zeros(film_l))
+        exit()
+
+    print("Performing XY correction.")
+
+    # Compute offsets between all pairs of sub images.
+    endpost = film_l - step/2
+    old_start1 = -1
+    start1 = 0
+    end1 = start1 + step
+    start2 = start1
+    end2 = start2 + step
+    i = 0
+    j = 0
+    centers = [(end1 - start1)/2 + start1]
+    pairs = []
+    while (start1 < endpost):
+
+        if (start2 > endpost):
+            i += 1
+            j = i
+            start1 += step
+            end1 = start1 + step
+            start2 = start1
+            end2 = start2 + step
+            if (end1 > endpost):
+                end1 = film_l
+            if (end2 > endpost):
+                end2 = film_l
+            if (start1 < endpost):
+                centers.append((end1 - start1)/2 + start1)
+
+        if (start1 > endpost):
+            continue
+
+        if not (start1 == start2):
+            if (old_start1 != start1):
+                i3_data.loadDataInFrames(fmin = start1, fmax = end1-1)
+                sub1 = i3_data.i3To2DGridAllChannelsMerged(uncorrected = True)
+                old_start1 = start1
+
+            i3_data.loadDataInFrames(fmin = start2, fmax = end2-1)
+            sub2 = i3_data.i3To2DGridAllChannelsMerged(uncorrected = True)
+
+            [corr, dx, dy, success] = imagecorrelation.xyOffset(sub1,
+                                                                sub2,
+                                                                scale)
+
+            dx = dx/float(scale)
+            dy = dy/float(scale)
+
+            print("offset between frame ranges ", start1, "-" , end1 , " and ", start2, "-", end2)
+
+            if success:
+                print(" -> ", dx, dy, "good")
+            else:
+                print(" -> ", dx, dy, "bad")
+            print("")
+
+            pairs.append([i, j, dx, dy, success])
+
+        j += 1
+        start2 += step
+        end2 = start2 + step
+        if (end2 > endpost):
+            end2 = film_l
+
+
+    print("--")
+
+    #
+    # For testing it is faster to not have to re-run the
+    # XY drift correction calculations.
+    #
+    #with open("test.dat", "w") as fp:
+    #    pickle.dump([centers, pairs], fp)
+    #
+    #with open("test.dat") as fp:
+    #    [centers, pairs] = pickle.load(fp)
+    #
+
+    # Prepare rij_x, rij_y, A matrix.
+    rij_x = numpy.zeros(len(pairs), dtype = numpy.float32)
+    rij_y = numpy.zeros(len(pairs), dtype = numpy.float32)
+    A = numpy.zeros((len(pairs),len(centers)), dtype = numpy.float32)
+    for i, pair in enumerate(pairs):
+        rij_x[i] = pair[2]
+        rij_y[i] = pair[3]
+        A[i,pair[0]:pair[1]] = 1.0
+
+    # Calculate drift (pass1). 
+    # dx and dy contain the optimal offset between sub image i and sub image i+1 in x/y.
+    pinv_A = numpy.linalg.pinv(A)
+    dx = numpy.dot(pinv_A, rij_x)
+    dy = numpy.dot(pinv_A, rij_y)
+
+    # Calculate errors.
+    err_x = numpy.dot(A, dx) - rij_x
+    err_y = numpy.dot(A, dy) - rij_y
+
+    err_d = numpy.sqrt(err_x * err_x + err_y * err_y)
+    arg_sort_err = numpy.argsort(err_d)
+
+    # Print errors before.
+    if 0:
+        print("Before:")
+        for i in range(err_d.size):
+            print(i, rij_x[i], rij_y[i], A[i,:], err_d[i])
+        print("")
+
+    # Remove bad values.
+    j = len(arg_sort_err) - 1
+
+    while (j > 0) and (err_d[arg_sort_err[j]] > max_err):
+        index = arg_sort_err[j]
+        delA = numpy.delete(A, index, 0)
+        if (numpy.linalg.matrix_rank(delA, tol = 1.0) == (len(centers)-1)):
+            print(j, "removing", index, "with error", err_d[index])
+            A = delA
+            rij_x = numpy.delete(rij_x, index, 0)
+            rij_y = numpy.delete(rij_y, index, 0)
+            err_d = numpy.delete(err_d, index, 0)
+            arg_sort_err[(arg_sort_err > index)] -= 1
+        else:
+            print("not removing", index, "with error", err_d[index])
+        j -= 1
+
+    # Print errors after.
+    if 0:
+        print("")
+        print("After:")
+        for i in range(err_d.size):
+            print(i, rij_x[i], rij_y[i], A[i,:], err_d[i])
+        print("")
+
+    # Calculate drift (pass2). 
+    pinv_A = numpy.linalg.pinv(A)
+    dx = numpy.dot(pinv_A, rij_x)
+    dy = numpy.dot(pinv_A, rij_y)
+
+
+    # Integrate to get final drift.
+    driftx = numpy.zeros((dx.size))
+    drifty = numpy.zeros((dy.size))
+    for i in range(dx.size):
+        driftx[i] = numpy.sum(dx[0:i])
+        drifty[i] = numpy.sum(dy[0:i])
+
+    if 1:
+        for i in range(driftx.size):
+            print(i, centers[i], driftx[i], drifty[i])
+
+    # Create spline for interpolation.
+    final_driftx = interpolateData(centers, driftx)
+    final_drifty = interpolateData(centers, drifty)
+
+    # Plot XY drift.
+    if 0:
+        import matplotlib
+        import matplotlib.pyplot as pyplot
+
+        x = numpy.arange(film_l)
+        fig = pyplot.figure()
+        ax = fig.add_subplot(111)
+        ax.plot(x, final_driftx, color = 'blue')
+        ax.plot(x, final_drifty, color = 'red')
+        pyplot.show()
+
+    # Z correction.
+    if not correct_z:
+        saveDriftData(final_driftx,
+                      final_drifty,
+                      numpy.zeros(film_l))
+        exit()
+
+    print("")
+    print("Performing Z Correction.")
+
+    start = 0
+    z_bins = 20
+    i3_data.loadDataInFrames(fmin = start, fmax = start+step)
+
+    if correct_z:
+        z_bins = 20
+        xyzmaster = i3_data.i3To3DGridAllChannelsMerged(z_bins,
+                                                        uncorrected = True)
+
+    j = 0
+    index = 0
+    old_dz = 0.0
+    driftz = numpy.zeros((dx.size))
+    while(j < film_l):
+
+        # Load correct frame range.
+        if ((j + 2*step) >= film_l):
+            i3_data.loadDataInFrames(fmin = j)
+            step_step = 2*step
+        else:
+            i3_data.loadDataInFrames(fmin = j, fmax = j + step)
+            step_step = step
+
+        # Apply XY drift correction.
+        i3_data.applyXYDriftCorrection(driftx[index], drifty[index])
+
+        # Z correlation
+        dz = old_dz
+
+        xyzcurr = i3_data.i3To3DGridAllChannelsMerged(z_bins,
+                                                      uncorrected = True)
+
+        [corr, fit, dz, z_success] = imagecorrelation.zOffset(xyzmaster, xyzcurr)
+
+        # Update Values
+        if z_success:
+            old_dz = dz
+        else:
+            dz = old_dz
+                
+        dz = dz * 1000.0/float(z_bins)
+        
+        if z_success:
+            i3_data.applyZDriftCorrection(-dz)
+            xyzmaster += i3_data.i3To3DGridAllChannelsMerged(z_bins)
+
+        driftz[index] = dz
+
+        if z_success:
+            print(index, dz, "good")
+        else:
+            print(index, dz, "bad")
+
+        index += 1
+        j += step_step
+
+    final_driftz = interpolateData(centers, driftz)
+
+    saveDriftData(final_driftx,
+                  final_drifty,
+                  final_driftz)
+
+    # Plot X,Y, Z drift.
+    if show_plot:
+        import matplotlib
+        import matplotlib.pyplot as pyplot
+
+        pixel_size = 160.0 # pixel size in nm.
+        x = numpy.arange(film_l)
+        fig = pyplot.figure()
+        ax = fig.add_subplot(111)
+        ax.plot(x, pixel_size * final_driftx, color = 'red')
+        ax.plot(x, pixel_size * final_drifty, color = 'green')
+        ax.plot(x, final_driftz, color = 'blue')
+        pyplot.show()
+
+
+if __name__ == "__main__":
+
+
+    parser = argparse.ArgumentParser(description='A Python implementation of the drift algorith')
+    
+    parser.add_argument('--bin', dest='bin', type=str, required=True)
+    parser.add_argument('--drift', dest='drift', type=str, required=True)
+    parser.add_argument('--step', dest='step', type=float, required=True)
+    parser.add_argument('--scale', dest='scale', type=float, required=True)
+    parser.add_argument('--zcorrect', dest='correct_z', type=bool, required=False, default=True)
+    parser.add_argument('--show_plot', dest='show_plot', type=bool, required=False, default=False)
+
+    args = parser.parse_args()
+
+    rcc(args.bin, args.drift, args.step, args.scale, correct_z=args.correct_z, show_plot=args.show_plot)
+
+#
+# The MIT License
+#
+# Copyright (c) 2014 Zhuang Lab, Harvard University
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
diff --git a/storm_analysis/test/run_tests.py b/storm_analysis/test/run_tests.py
index bba2d763..ed324e46 100644
--- a/storm_analysis/test/run_tests.py
+++ b/storm_analysis/test/run_tests.py
@@ -21,25 +21,32 @@
     [dao_exe, "test.dax", "test_3d_2d.bin", "test_3d_2d.xml"],
     [dao_exe, "test.dax", "test_3d_3d.bin", "test_3d_3d.xml"],
     [dao_exe, "test.dax", "test_3d_Z.bin", "test_3d_Z.xml"],
-    ["Testing FRC"],
-    ["../frc/frc_calc2d.py", "test_drift_mlist.bin", "test_drift_frc.txt", "0"],
+
+    #["Testing FRC"],
+    #["../frc/frc_calc2d.py", "test_drift_mlist.bin", "test_drift_frc.txt", "0"],
+
     ["Testing L1H"],
     ["../L1H/setup_A_matrix.py", "theoritical", "test_l1h", "1.0", "0"],
     ["../L1H/cs_analysis.py", "test_l1h.dax", "test_l1h.xml", "test_l1h.hres", "test_l1h_list.bin"],
-    ["Testing RCC"],
-    ["../rcc/rcc-drift-correction.py", "test_drift_mlist.bin", "test_drift.txt", "2000", "1"],
+
+    #["Testing RCC"],
+    #["../rcc/rcc-drift-correction.py", "test_drift_mlist.bin", "test_drift.txt", "2000", "1"],
+
     ["Testing Rolling Ball Background Subtraction"],
     ["../rolling_ball_bgr/rolling_ball.py", "test_bg_sub.dax", "test_bg_sub_rb.dax", "10", "1"],
+
     ["Testing sCMOS"],
     [scmos_exe, "test.dax", "test_sc_2d_fixed.bin", "test_sc_2d_fixed.xml"],
     [scmos_exe, "test.dax", "test_sc_2d.bin", "test_sc_2d.xml"],
     [scmos_exe, "test.dax", "test_sc_3d.bin", "test_sc_3d.xml"],
     [scmos_exe, "test.dax", "test_sc_Z.bin", "test_sc_Z.xml"],
+
     ["Testing Spliner"],
     ["../spliner/measure_psf.py", "test_spliner.dax", "none", "test_spliner_olist.bin", "test_spliner_psf.psf", "1"],
     ["../spliner/psf_to_spline.py", "test_spliner_psf.psf", "test_spliner_psf.spline", "10"],
     [spliner_exe, "test_spliner.dax", "test_spliner_slist.bin", "test_spliner_dh.xml"],
     [spliner_exe, "test_spliner.dax", "test_spliner_flist.bin", "test_spliner_dh_fista.xml"],
+
     ["Testing Track/Average/Correct"],
     ["../sa_utilities/track_average_correct.py", "test_drift_mlist.bin", "test_drift_alist.bin", "test_drift.xml"],
     
@@ -47,9 +54,11 @@
     ["Testing DBSCAN Clustering"],
     ["../dbscan/dbscan_analysis.py", "test_drift_alist.bin", "0"],
     ["../dbscan/cluster_images.py", "test_drift_aclusters_list.bin", "DBSCAN Clustering", "50", "20", "test_drift_dbscan"],
+
     ["Testing Voronoi Clustering"],
     ["../voronoi/voronoi_analysis.py", "test_drift_alist.bin", "1.25", "./"],
     ["../dbscan/cluster_images.py", "test_drift_asrt_list.bin", "Voronoi Clustering", "50", "20", "test_drift_vr"],
+
     ["Testing Wavelet Background Subtraction"],
     ["../wavelet_bgr/wavelet_bgr.py", "test_bg_sub.dax", "test_bg_sub_wbgr.dax", "db4", "2", "2", "10"]
 ]
diff --git a/storm_analysis/test/test_c_extensions_import.py b/storm_analysis/test/test_c_extensions_import.py
index 7052d8fb..4f513525 100644
--- a/storm_analysis/test/test_c_extensions_import.py
+++ b/storm_analysis/test/test_c_extensions_import.py
@@ -3,7 +3,7 @@
 import platform
 
 def test_c_extensions_import():
-	# Try to import all C extension
+	"Try to import all C extension"
 	
 	import storm_analysis.sa_library.ia_utilities_c
 	import storm_analysis.sa_library.multi_fit_c
diff --git a/storm_analysis/test/test_frc.py b/storm_analysis/test/test_frc.py
new file mode 100644
index 00000000..f6074aca
--- /dev/null
+++ b/storm_analysis/test/test_frc.py
@@ -0,0 +1,14 @@
+import storm_analysis
+
+
+def test_frc():
+	
+	in_list = storm_analysis.get_data("test/data/test_drift_mlist.bin")
+	results = storm_analysis.get_path_output_test("test_drift_frc.txt")
+
+	from storm_analysis.frc.frc_calc2d import calc2d
+	calc2d(in_list, results, False)
+
+
+if __name__ == "__main__":
+	test_frc()
\ No newline at end of file
diff --git a/storm_analysis/test/test_rcc.py b/storm_analysis/test/test_rcc.py
new file mode 100644
index 00000000..7b347b7a
--- /dev/null
+++ b/storm_analysis/test/test_rcc.py
@@ -0,0 +1,14 @@
+import storm_analysis
+
+
+def test_rcc():
+	
+	bin = storm_analysis.get_data("test/data/test_drift_mlist.bin")
+	drift = storm_analysis.get_path_output_test("test_drift.txt")
+
+	from storm_analysis.rcc.rcc_drift_correction import rcc
+	rcc(bin, drift, 2000, 1)
+
+
+if __name__ == "__main__":
+	test_rcc()
\ No newline at end of file