setup.py

.gitignore

@@ -3,6 +3,12 @@
 #############
 
 *.py[co]
+*.egg-info
+build/
+*.eggs
+dist/
+.cache/
+storm_analysis/test/output/
 
 #############
 ## Emacs

MANIFEST.in

@@ -0,0 +1,14 @@
+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*
+
+prune storm_analysis/test/output
+

setup.cfg

@@ -0,0 +1,2 @@
+[aliases]
+test=pytest

setup.py

@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import platform
+import os
+import sys
+
+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():
+
+    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", ["./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"],
+                            libraries=library_dirs, include_dirs=include_dirs),
+                  Extension("storm_analysis.sa_library._multi_fit", ["./storm_analysis/sa_library/multi_fit.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", ["./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),
+
+                  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':
+        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(
+    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={},
+    exclude_package_data={},
+    include_package_data=True,
+
+    requires=[],
+
+    setup_requires=['pytest-runner'],
+    tests_require=['pytest'],
+
+    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',
+    ],
+)

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):

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()

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

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
 

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):

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),

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)]

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),