Format tests with black and update to work with current scipy

tests/Stoner/Image/test_folder.py

@@ -2,46 +2,63 @@
 """Stiner.Image.folders test
 """
 
-from Stoner import Data
-from Stoner.Image import ImageArray, ImageFolder, ImageStack
-import numpy as np
+from Stoner.Image import ImageArray, ImageFolder
 import pytest
-from os import path
 import os
 
-knownkeys = ['Averaging', 'Comment:', 'Contrast Shift', 'HorizontalFieldOfView',
-             'Lens', 'Loaded from', 'Magnification', 'MicronsPerPixel', 'field: units',
-             'field: units', 'filename', 'subtraction']
-knownfieldvals = [-233.432852, -238.486666, -243.342465, -248.446173,
-                  -253.297813, -258.332918, -263.340476, -268.20511]
+knownkeys = [
+    "Averaging",
+    "Comment:",
+    "Contrast Shift",
+    "HorizontalFieldOfView",
+    "Lens",
+    "Loaded from",
+    "Magnification",
+    "MicronsPerPixel",
+    "field: units",
+    "field: units",
+    "filename",
+    "subtraction",
+]
+knownfieldvals = [
+    -233.432852,
+    -238.486666,
+    -243.342465,
+    -248.446173,
+    -253.297813,
+    -258.332918,
+    -263.340476,
+    -268.20511,
+]
 
-testdir=os.path.join(os.path.dirname(__file__),"coretestdata","testims")
-fldr=ImageFolder(testdir, pattern="*.png")
+testdir = os.path.join(os.path.dirname(__file__), "coretestdata", "testims")
+fldr = ImageFolder(testdir, pattern="*.png")
 
 
 def test_load():
-    fldr=ImageFolder(testdir, pattern="*.png")
-    assert len(fldr)==len(os.listdir(testdir)), "Didn't find all the images"
-    stack=fldr.as_stack()
-    assert len(stack)==len(fldr),"Conversion to ImageStack with as_stack() failed to preserve length"
+    fldr = ImageFolder(testdir, pattern="*.png")
+    assert len(fldr) == len(os.listdir(testdir)), "Didn't find all the images"
+    stack = fldr.as_stack()
+    assert len(stack) == len(fldr), "Conversion to ImageStack with as_stack() failed to preserve length"
+
 
 def test_properties():
-    fldr=ImageFolder(testdir, pattern="*.png")
-    assert fldr.size==(512, 672),f"fldr.size incorrect at {fldr.size}"
-    empty=ImageFolder()
-    assert empty.size==tuple(),f"Empty folder.size wrong at {empty.size}"
-    fldr[1]=fldr[1].crop(4)
-    assert not fldr.size,f"fldr.size didn't return False for non-uniform images, got {fldr.size}"
+    fldr = ImageFolder(testdir, pattern="*.png")
+    assert fldr.size == (512, 672), f"fldr.size incorrect at {fldr.size}"
+    empty = ImageFolder()
+    assert empty.size == tuple(), f"Empty folder.size wrong at {empty.size}"
+    fldr[1] = fldr[1].crop(4)
+    assert not fldr.size, f"fldr.size didn't return False for non-uniform images, got {fldr.size}"
     for im in fldr.images:
-        assert isinstance(im,ImageArray),"fldr.images returned something that wasn't an image array"
+        assert isinstance(im, ImageArray), "fldr.images returned something that wasn't an image array"
+
 
 def test_methods():
-    fldr=ImageFolder(testdir, pattern="*.png")
-    assert len(list(fldr.loaded))==0,"ImageFolder got loaded unexpectedly!"
+    fldr = ImageFolder(testdir, pattern="*.png")
+    assert len(list(fldr.loaded)) == 0, "ImageFolder got loaded unexpectedly!"
     fldr.loadgroup()
-    assert len(list(fldr.loaded))==8,"ImageFolder.looadgroup() failed to load!"
-
+    assert len(list(fldr.loaded)) == 8, "ImageFolder.looadgroup() failed to load!"
 
 
-if __name__=="__main__":
-    pytest.main(["--pdb",__file__])
+if __name__ == "__main__":
+    pytest.main(["--pdb", __file__])

tests/Stoner/Image/test_kerr.py

@@ -5,95 +5,100 @@
 @author: phyrct
 """
 
-from Stoner.Image import ImageArray, ImageFile
-from Stoner.Image.kerr import KerrArray, KerrImageFile,KerrStack
-from Stoner.Core import typeHintedDict
-from Stoner import Data,__home__
+from Stoner.Image.kerr import KerrArray, KerrImageFile, KerrStack
+from Stoner import Data, __home__
 import numpy as np
 import pytest
-import sys
-from os import path
 import os
 import matplotlib.pyplot as plt
 
-import warnings
 
 import Stoner
+
 Stoner.Options.multiprocessing = False
 
-#data arrays for testing - some useful small images for tests
+# data arrays for testing - some useful small images for tests
 
-testdir=os.path.join(os.path.dirname(__file__),"kerr_testdata")
-testdir2=os.path.join(os.path.dirname(__file__),"coretestdata","testims")
-sample_data_dir=os.path.join(__home__,"../sample-data")
+testdir = os.path.join(os.path.dirname(__file__), "kerr_testdata")
+testdir2 = os.path.join(os.path.dirname(__file__), "coretestdata", "testims")
+sample_data_dir = os.path.join(__home__, "../sample-data")
 
 
 def shares_memory(arr1, arr2):
     """Check if two numpy arrays share memory"""
-    #ret = arr1.base is arr2 or arr2.base is arr1
+    # ret = arr1.base is arr2 or arr2.base is arr1
     ret = np.may_share_memory(arr1, arr2)
     return ret
 
-selfimage=KerrArray(os.path.join(testdir,"kermit3.png"),ocr_metadata=True)
-selfimage2=KerrArray(os.path.join(testdir,"kermit3.png"))
-selfimage3=KerrImageFile(os.path.join(sample_data_dir,"testnormalsave.png"))
+
+selfimage = KerrArray(os.path.join(testdir, "kermit3.png"), ocr_metadata=True)
+selfimage2 = KerrArray(os.path.join(testdir, "kermit3.png"))
+selfimage3 = KerrImageFile(os.path.join(sample_data_dir, "testnormalsave.png"))
 selfks = KerrStack(testdir2)
 
+
 def test_kerr_ops():
     im = selfimage3.clone
-    assert isinstance(im.image,KerrArray),"KerrImageFile not blessing the image property correctly"
-    im1=im.float_and_croptext()
-    assert isinstance(im1.image,KerrArray),"Calling a crop routine without the _ argument returns a new KerrArray"
-    im2=im.float_and_croptext(_=True)
-    assert im2==im,"Calling crop method with _ argument changed the KerrImageFile"
-    im=KerrImageFile(selfimage2.clone)
+    assert isinstance(im.image, KerrArray), "KerrImageFile not blessing the image property correctly"
+    im1 = im.float_and_croptext()
+    assert isinstance(im1.image, KerrArray), "Calling a crop routine without the _ argument returns a new KerrArray"
+    im2 = im.float_and_croptext(_=True)
+    assert im2 == im, "Calling crop method with _ argument changed the KerrImageFile"
+    im = KerrImageFile(selfimage2.clone)
     im.float_and_croptext(_=True)
-    mask=im.image.defect_mask_subtract_image()
-    im.image[~mask]=np.mean(im.image[mask])
-    selim=im
-    assert mask.sum()==343228,"Mask didn't work out right"
-    im=KerrImageFile(selfimage2.clone)
+    mask = im.image.defect_mask_subtract_image()
+    im.image[~mask] = np.mean(im.image[mask])
+    _ = im
+    assert mask.sum() == 343228, "Mask didn't work out right"
+    im = KerrImageFile(selfimage2.clone)
     im.float_and_croptext(_=True)
-    mask=im.image.defect_mask(radius=4)
-    im.image[~mask]=np.mean(im.image[mask])
-    selim2=im
-    assert mask.sum()==342540,"Mask didn't work out right"
+    mask = im.image.defect_mask(radius=4)
+    im.image[~mask] = np.mean(im.image[mask])
+    selim2 = im
+    assert mask.sum() == 342540, "Mask didn't work out right"
     selim2.level_image()
     selim2.remove_outliers()
     selim2.normalise()
     selim2.plot_histogram()
     selim2.imshow()
-    assert len(plt.get_fignums())==2,"Didn't open the correct number of figures"
+    assert len(plt.get_fignums()) == 2, "Didn't open the correct number of figures"
     plt.close("all")
 
 
-
-
 def test_tesseract_ocr():
-    #this incidentally tests get_metadata too
+    # this incidentally tests get_metadata too
     if not selfimage.tesseractable:
-        print("#"*80)
+        print("#" * 80)
         print("Skipping test that uses tesseract.")
         return None
-    m=selfimage.metadata
+    _ = selfimage.metadata
 
     # assert all((m['ocr_scalebar_length_microns']==50.0,
     #                     m['ocr_date']=='11/30/15',
     #                     m['ocr_field'] == -0.13)), 'Misread metadata {}'.format(m))
-    keys=('ocr_scalebar_length_pixels', 'ocr_field_of_view_microns',
-                      'Loaded from', 'ocr_microns_per_pixel', 'ocr_pixels_per_micron')
+    _ = (
+        "ocr_scalebar_length_pixels",
+        "ocr_field_of_view_microns",
+        "Loaded from",
+        "ocr_microns_per_pixel",
+        "ocr_pixels_per_micron",
+    )
     # assert all([k in m.keys() for k in keys]), 'some part of the metadata didn\'t load {}'.format(m))
-    m_un=selfimage2.metadata
-    assert 'ocr_field' not in m_un.keys(), 'Unannotated image has wrong metadata'
+    m_un = selfimage2.metadata
+    assert "ocr_field" not in m_un.keys(), "Unannotated image has wrong metadata"
+
 
 def test_kerrstack():
-    print("X"*80+"\n"+"Test Kerrstack")
-    ks=selfks.clone
-    ks.each.normalise(scale=(0,1.0))
-    assert np.min(ks.imarray)==0.0 and np.max(ks.imarray)==1.0, 'KerrStack subtract failed min,max: {},{}'.format(np.min(ks.imarray),np.max(ks.imarray))
-    d=ks.hysteresis()
+    print("X" * 80 + "\n" + "Test Kerrstack")
+    ks = selfks.clone
+    ks.each.normalise(scale=(0, 1.0))
+    assert np.min(ks.imarray) == 0.0 and np.max(ks.imarray) == 1.0, "KerrStack subtract failed min,max: {},{}".format(
+        np.min(ks.imarray), np.max(ks.imarray)
+    )
+    d = ks.hysteresis()
     assert isinstance(d, Data), "hysteresis didn't return Data"
-    assert d.data.shape==(len(ks),2), "hysteresis didn't return correct shape"
+    assert d.data.shape == (len(ks), 2), "hysteresis didn't return correct shape"
+
 
-if __name__=="__main__": # Run some tests manually to allow debugging
-    pytest.main(["--pdb",__file__])
+if __name__ == "__main__":  # Run some tests manually to allow debugging
+    pytest.main(["--pdb", __file__])