Fix names that do not resolve, and drop Python 2

storm_analysis/L1H/setup_A_matrix.py

@@ -12,7 +12,6 @@
 import pickle
 import scipy.io
 from scipy.interpolate import griddata
-import sys
 
 
 def createCoordinates(inner_size, scale, boundary_scale, pad = [0,0]):
@@ -232,13 +231,7 @@ def loadAMatrix(file_name):
 
     with open(file_name, 'rb') as fp:
 
-        # Python 3
-        if (sys.version_info > (3, 0)):
-            matrix = pickle.load(fp, encoding='latin1')
-
-        # Python 2
-        else:
-            matrix = pickle.load(fp)
+        matrix = pickle.load(fp, encoding='latin1')
 
     return matrix
 

storm_analysis/admm/admm_lasso_c.py

@@ -160,7 +160,7 @@ def newImage(self, image, background):
         c_image = numpy.ascontiguousarray(image_no_bg, dtype=numpy.float64)
         admm_lasso.newImage(self.c_admm_lasso, c_image)
 
-    def run(self, a_lamba, iterations):
+    def run(self, a_lambda, iterations):
         admm_lasso.run(self.c_admm_lasso, a_lambda, iterations)
 
 

storm_analysis/diagnostics/spliner_configure_common.py

@@ -23,8 +23,6 @@
 import storm_analysis.spliner.measure_psf_utils as measurePSFUtils
 import storm_analysis.spliner.psf_to_spline as psfToSpline
 
-import storm_analysis.diagnostics.spliner.settings as settings
-
 
 def configure(settings, use_dh, no_splines):
 

storm_analysis/jupyter_examples/multiplane_measure_psf.py

@@ -221,5 +221,5 @@ def sCMOSSingleFrameXML():
     makeCMOSCalibration()
     makeMapping()
     makeSampleData()
-    sCMOSSinglePlaneXML()
+    sCMOSSingleFrameXML()
 

storm_analysis/multi_plane/analysis_io.py

@@ -6,12 +6,12 @@
 """
 import numpy
 import os
-import sys
 
 from xml.etree import ElementTree
 
 import storm_analysis.sa_library.analysis_io as analysisIO
 import storm_analysis.sa_library.sa_h5py as saH5Py
+import storm_analysis.sa_library.static_background as static_background
 
 import storm_analysis.multi_plane.mp_utilities as mpUtil
 
@@ -56,10 +56,7 @@ def __init__(self, parameters = None, sa_type = None, **kwds):
 
             # Save analysis parameters.
             etree = parameters.toXMLElementTree(False)
-            if (sys.version_info > (3, 0)):
-                self.h5.addMetadata(ElementTree.tostring(etree, 'unicode'))
-            else:
-                self.h5.addMetadata(ElementTree.tostring(etree, 'ISO-8859-1'))
+            self.h5.addMetadata(ElementTree.tostring(etree, 'unicode'))
 
             # Save pixel size.
             self.h5.setPixelSize(parameters.getAttr("pixel_size"))

storm_analysis/multi_plane/fitting_mp.py

@@ -600,9 +600,9 @@ def setVariances(self, variances):
 
             # Save a pictures of the PSFs for debugging purposes.
             if self.check_mode:
-                print("psf max", numpy.max(psf))
-                filename = "psf_z0.0_c{1:d}.tif".format(j)
-                tifffile.imwrite(filename, psf.astype(numpy.float32))
+                print("psf max", numpy.max(psf_norm))
+                filename = "psf_z0.0_c{0:d}.tif".format(i)
+                tifffile.imwrite(filename, psf_norm.astype(numpy.float32))
 
         # This handles the rest of the initialization.
         #

storm_analysis/multi_plane/mp_fit_arb_c.py

@@ -103,7 +103,7 @@ def setWeights(self, weights, verbose = True):
                        "x" : numpy.ones((2, self.n_channels))/float(self.n_channels),
                        "y" : numpy.ones((2, self.n_channels))/float(self.n_channels),
                        "z" : numpy.ones((2, self.n_channels))/float(self.n_channels)}
-            super(MPSFFnFit, self).setWeights(weights, 0.0, 0.0, verbose = verbose)
+            super(MPPSFFnFit, self).setWeights(weights, 0.0, 0.0, verbose = verbose)
 
         else:
             zmax = self.psf_objects[0].getZMax() * 1.0e-3

storm_analysis/rolling_ball_bgr/rolling_ball_lib_c.py

@@ -11,7 +11,6 @@
 import scipy.ndimage
 
 import ctypes
-import numpy
 from numpy.ctypeslib import ndpointer
 
 import storm_analysis.sa_library.loadclib as loadclib

storm_analysis/sa_library/analysis_io.py

@@ -7,7 +7,6 @@
 """
 import numpy
 import os
-import sys
 
 from xml.etree import ElementTree
 
@@ -156,10 +155,7 @@ def __init__(self, parameters = None, sa_type = None, **kwds):
 
             # Save analysis parameters.
             etree = parameters.toXMLElementTree(False)
-            if (sys.version_info > (3, 0)):
-                self.h5.addMetadata(ElementTree.tostring(etree, 'unicode'))
-            else:
-                self.h5.addMetadata(ElementTree.tostring(etree, 'ISO-8859-1'))
+            self.h5.addMetadata(ElementTree.tostring(etree, 'unicode'))
 
             # Save pixel size.
             self.h5.setPixelSize(parameters.getAttr("pixel_size"))

storm_analysis/sa_library/loadclib.py

@@ -44,10 +44,7 @@ def loadCLibrary(library_filename):
             ctypes.windll.kernel32.SetErrorMode(0)
 
             # Push the storm-analysis directory into the DLL search path.
-            if (sys.version_info > (3, 0)):
-                ctypes.windll.kernel32.SetDllDirectoryW(c_lib_path)
-            else:
-                ctypes.windll.kernel32.SetDllDirectoryW(unicode(c_lib_path))
+            ctypes.windll.kernel32.SetDllDirectoryW(c_lib_path)
 
             # Try to load the library.
             c_lib = ctypes.cdll.LoadLibrary(os.path.join(c_lib_path, library_filename))

storm_analysis/sa_utilities/bin_to_hdf5.py

@@ -8,7 +8,6 @@
 Hazen 12/17
 """
 import os
-import sys
 
 from xml.etree import ElementTree
 
@@ -55,10 +54,7 @@ def BinToHDF5(bin_name, hdf5_name):
 
         # Set metadata.
         if params_xml is not None:
-            if (sys.version_info > (3, 0)):
-                h5.addMetadata(ElementTree.tostring(params_xml, 'unicode'))
-            else:
-                h5.addMetadata(ElementTree.tostring(params_xml, 'ISO-8859-1'))
+            h5.addMetadata(ElementTree.tostring(params_xml, 'unicode'))
 
         # Convert data.
         i3 = readinsight3.I3Reader(bin_name)

storm_analysis/simulator/emitters_on_lines.py

@@ -133,7 +133,7 @@ def emittersOnLines(h5_name, nlines, nemitters, sx = 256, sy = 256, maxl = 200,
 
     emittersOnLines(args.hdf5,
                     args.nlines,
-                    argls.nemitters,
+                    args.nemitters,
                     sx = args.sx,
                     sy = args.sy,
                     maxl = args.maxl,

storm_analysis/simulator/pupil_math.py

@@ -184,7 +184,7 @@ def aberrationOPD(self, z_stage, z_p, smp_index):
         sin_theta_1 = (self.wavelength/self.imm_index)*self.k
         theta_1 = numpy.arcsin(sin_theta_1 + 0j)
 
-        sin_theta_2 = (n1/n2)*sin_theta_1
+        sin_theta_2 = (self.imm_index/smp_index)*sin_theta_1
         theta_2 = numpy.arcsin(sin_theta_2 + 0j)
 
         z_o = smp_index/self.imm_index * z_stage
@@ -206,7 +206,7 @@ def aberrationOPD(self, z_stage, z_p, smp_index):
         # decrease exponentially with increasing distance from coverslip.
         #
         pf_ab = numpy.exp(-1j * t4)
-        return self.appylNARestriction(pf_ab)
+        return self.applyNARestriction(pf_ab)
 
     def applyNARestriction(self, pupil_fn):
         """

storm_analysis/spliner/spline1D.py

@@ -97,7 +97,7 @@ def f(self, x):
 
     xv = []
     yv = []
-    for i in range(x.size/10):
+    for i in range(x.size//10):
         xv.append(x[i*10])
         yv.append(y[i*10])
     xv.append(x[-1])
@@ -120,5 +120,5 @@ def f(self, x):
     pw.plot(x,ys)
     #pw.plot(x,dxs)
 
-    raw_input("return to continue")
+    input("return to continue")
 

storm_analysis/test/test_clusters_sa_h5py.py

@@ -343,6 +343,8 @@ def test_cl_sa_h5py_7():
     test_cl_sa_h5py_5()
     test_cl_sa_h5py_6()
     test_cl_sa_h5py_7()
+    test_cl_sa_h5py_z_is_loaded()
+    test_cl_sa_h5py_drops_invalid_z()
 
 
 

storm_analysis/test/test_drift_correction.py

@@ -480,7 +480,8 @@ def test_drift_correction_10():
 
 
 if (__name__ == "__main__"):
-    _test_drift_correction_1()
+    test_drift_correction_1()
+    test_drift_correction_1_xy_failure()
     test_drift_correction_2()
     test_drift_correction_3()
     test_drift_correction_4()

storm_analysis/test/test_fitting_mp.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+"""
+Tests of multi_plane.fitting_mp
+"""
+import glob
+import numpy
+import os
+import pickle
+import tifffile
+
+import storm_analysis
+import storm_analysis.sa_library.fitting as fitting
+import storm_analysis.sa_library.parameters as parameters
+
+import storm_analysis.multi_plane.fitting_mp as fittingMp
+
+
+im_size = (20, 18)
+n_channels = 2
+
+
+def configureTest():
+    """
+    Build the parameters and the mapping file that MPPeakFinderDao needs.
+    """
+    map_name = storm_analysis.getPathOutputTest("test_fitting_mp.map")
+
+    mappings = {}
+    for i in range(n_channels):
+        mappings["0_" + str(i) + "_x"] = numpy.array([0.0, 1.0, 0.0])
+        mappings["0_" + str(i) + "_y"] = numpy.array([0.0, 0.0, 1.0])
+        mappings[str(i) + "_0_x"] = numpy.array([0.0, 1.0, 0.0])
+        mappings[str(i) + "_0_y"] = numpy.array([0.0, 0.0, 1.0])
+    with open(map_name, "wb") as fp:
+        pickle.dump(mappings, fp)
+
+    params = parameters.ParametersMultiplaneDao()
+    params.setAttr("background_sigma", "float", 8.0)
+    params.setAttr("find_max_radius", "int", 2)
+    params.setAttr("foreground_sigma", "float", 1.5)
+    params.setAttr("iterations", "int", 1)
+    params.setAttr("mapping", "filename", map_name)
+    params.setAttr("no_fitting", "int", 0)
+    params.setAttr("pixel_size", "float", 100.0)
+    params.setAttr("roi_size", "int", 10)
+    params.setAttr("sigma", "float", 1.5)
+    params.setAttr("threshold", "float", 6.0)
+
+    return params
+
+
+def test_fitting_mp_check_mode():
+    """
+    MPPeakFinderDao.setVariances() saves a picture of each channel's PSF
+    when check_mode is on.
+
+    That block was copied from the arbitrary PSF version, where the PSF is
+    called 'psf' and the channel index is 'j'. Here the PSF is 'psf_norm'
+    and the index is 'i', so it raised NameError, and the filename kept
+    "{1:d}" from the two argument version, so it would have raised
+    IndexError once the names were fixed.
+    """
+    params = configureTest()
+
+    # check_mode writes into the working directory.
+    cwd = os.getcwd()
+    os.chdir(storm_analysis.getPathOutputTest(""))
+    try:
+        for name in glob.glob("psf_z0.0_c*.tif"):
+            os.remove(name)
+
+        finder = fittingMp.MPPeakFinderDao(parameters = params,
+                                           n_channels = n_channels)
+        finder.check_mode = True
+
+        variances = [numpy.ones(im_size) for i in range(n_channels)]
+        finder.setVariances(variances)
+
+        # One image per channel, named by the channel index.
+        written = sorted(glob.glob("psf_z0.0_c*.tif"))
+        assert(written == ["psf_z0.0_c0.tif", "psf_z0.0_c1.tif"])
+
+        # And it is the normalized PSF that was saved, computed here
+        # independently of the finder. The variances are padded by the
+        # margin before the filters are built.
+        padded = (im_size[0] + 2*finder.margin, im_size[1] + 2*finder.margin)
+        expected = fitting.gaussianPSF(padded, 1.5).astype(numpy.float32)
+
+        for name in written:
+            psf = tifffile.imread(name)
+            assert(psf.shape == padded)
+            assert(numpy.allclose(psf, expected))
+    finally:
+        os.chdir(cwd)
+
+
+if (__name__ == "__main__"):
+    test_fitting_mp_check_mode()

storm_analysis/test/test_fitz_c.py

@@ -271,4 +271,6 @@ def test_fitz_c_5():
     test_fitz_c_3()
     test_fitz_c_4()
     test_fitz_c_5()
+    test_fitz_c_marker_survives_drift()
+    test_fitz_c_marker_propagates_to_tracks()
 

storm_analysis/test/test_pupil_math.py

@@ -82,9 +82,51 @@ def test_pupil_math_5():
     psf_c = geo_c.pfToPSF(pf, z_vals, scaling_factor = gsf)
 
 
+def test_pupil_math_aberration_opd():
+    """
+    aberrationOPD() had two names wrong and could not run at all.
+
+    sin_theta_2 was computed from n1 and n2, neither of which exists, and
+    the return statement called self.appylNARestriction(). The first
+    raised NameError, and fixing only that moved the failure to an
+    AttributeError from the second.
+
+    Snell's law here is between the immersion medium and the sample,
+    which is what the sibling aberration() uses:
+
+        sin_theta_2 = (self.imm_index/smp_index)*sin_theta_1
+
+    This geometry deliberately puts most of the grid outside the NA, so
+    that the restriction being applied is observable rather than vacuous.
+    """
+    geo = pupilMath.Geometry(32, 0.05, 0.6, 1.5, 1.2)
+
+    # applyNARestriction() masks on the normalized radius, geo.r > 1.0.
+    # geo.r_max is a different quantity, the NA edge in grid units.
+    outside = (geo.r > 1.0)
+    assert(numpy.count_nonzero(outside) > 0)
+
+    ab = geo.aberrationOPD(1.0, 0.5, 1.33)
+
+    assert(ab.shape == (32, 32))
+    assert(numpy.all(numpy.isfinite(ab)))
+
+    # applyNARestriction() zeros everything beyond the NA.
+    assert(numpy.all(ab[outside] == 0.0))
+    assert(numpy.any(ab[~outside] != 0.0))
+
+    # At zero defocus and a matched sample index there is no aberration,
+    # so the function is identically 1 inside the NA.
+    flat = geo.aberrationOPD(0.0, 0.0, 1.5)
+    assert(numpy.allclose(flat[~outside], 1.0 + 0j))
+
+
 if (__name__ == "__main__"):
     test_pupil_math_1()
     test_pupil_math_2()
     test_pupil_math_3()
+    test_pupil_math_4()
+    test_pupil_math_5()
+    test_pupil_math_aberration_opd()