add json lib; update unit tests; add lfs

.gitattributes

+*.nii.gz filter=lfs diff=lfs merge=lfs -text

tests/fslstats/feedsRun

@@ -53,6 +53,8 @@ options = [
     {"option": "-v", "expected": "1000 1000.000000"},
     {"option": "-V", "expected": "1000 1000.000000"},
     {"option": "-m", "expected": "0.495922"},
+    {"option": "-m -a", "expected": "0.495922"},
+    {"option": "-m -a -n", "expected": "0.495922"},
     {"option": "-M", "expected": "0.495922"},
     {"option": "-s", "expected": "0.290744"},
     {"option": "-S", "expected": "0.290744"},
@@ -63,6 +65,12 @@ options = [
     {"option": "-C", "expected": "4.498706 4.545873 4.613188"},
     {"option": "-p 50", "expected": "0.482584"},
     {"option": "-P 50", "expected": "0.482584"},
+    {"option": "-m -h 10 -c", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000 \n 4.498706 4.545873 4.613188"},
+    {"option": "-m -h 10", "expected": "0.495922 101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+    {"option": "-h 10", "expected": "101.000000 \n99.000000 \n108.000000 \n107.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+    {"option": "-H 10 0 1", "expected": "98.000000 \n102.000000 \n107.000000 \n108.000000 \n102.000000 \n93.000000 \n99.000000 \n88.000000 \n95.000000 \n108.000000"},
+    {"option": "-l 0.25 -u 0.75 -m", "expected": "0.495150"},
+    {"option": "-d imageForDiff.nii.gz -m", "expected": "0.000000"},
 ]
 
 # create a list of tests and expected results
@@ -82,55 +90,24 @@ tests_with_preoptions = [
         "preoptions": "-K",
         "mask": "mask.nii.gz",
         "options": "-m",
-        "expected": "0.948930 \n0.947671 \n1.003258 \n1.010696",
+        "expected": "1.078044 \n1.028827 \n0.986428 \n1.020869",
     },
     {
         "preoptions": "-t -K",
         "mask": "mask.nii.gz",
         "options": "-m",
-        "expected": "0.459736 \n0.476035 \n0.504080 \n0.549485 \n0.489194 \n0.471636 \n0.499178 \n0.461211",
+        "expected": "0.526682 \n0.515652 \n0.492337 \n0.511661 \n0.551362 \n0.513176 \n0.494091 \n0.509208",
     },
     {
         "preoptions": "-t",
         "mask": "",
         "options": "-m",
-        "expected": "0.496675 \n0.487950",
+        "expected": "0.503236 \n0.504035",
     },
 ]
 
-# taken from fslchpixdim test
-def create_image(shape, pixdim):
-    pixdim = list(pixdim)
-    data   = np.random.random(shape).astype(np.float32)
-    hdr    = nib.Nifti1Header()
-    hdr.set_data_dtype(np.float32)
-    hdr.set_data_shape(shape)
-    hdr.set_zooms(pixdim[:len(shape)])
-
-    return nib.Nifti1Image(data, np.eye(4), hdr)
-
-def create_mask(input_img, n_rois=4):
-    '''
-    Create a mask image from the input image.
-    The mask image will have n_rois different values with random sizes randomly placed in the image.
-    '''
-    data = input_img.get_fdata()
-    mask = np.zeros_like(data)
-    for i in range(n_rois + 1):
-        roi_size = np.random.randint(1, data.size)
-        roi_value = i
-        roi = np.random.choice(data.size, roi_size, replace=False)
-        mask.flat[roi] = roi_value
-    return nib.Nifti1Image(mask, input_img.affine, input_img.header)
-
-
 def test_fslstats():
     imgfile = 'test.nii.gz'
-    shape   = (10,10,10)
-    img     = create_image(shape, [1] * len(shape))
-    img.to_filename(imgfile)
-    mask = create_mask(img)
-    mask.to_filename('mask.nii.gz')
 
     # run the tests witoout preoptions
     for test in tests:
@@ -151,9 +128,6 @@ def test_fslstats():
 
     # run the tests with preoptions
     imgfile = 'test_4d.nii.gz'
-    shape   = (10,10,10, 2)
-    img     = create_image(shape, [1] * len(shape))
-    img.to_filename(imgfile)
     for test in tests_with_preoptions:
         cmd = f"fslstats {test['preoptions']} {test['mask']} {imgfile} {test['options']}"
         # remove any double spaces from empty test options
@@ -175,6 +149,4 @@ def test_fslstats():
 
 
 if __name__ == "__main__":
-    if len(sys.argv) > 1:
-        os.chdir(sys.argv[1])
     test_fslstats()