Merge pull request #380 from dchorel/Fix_concatenate_3D_with_4D_images

[WIP] Concatenate 3d with 4d images into a 4d image

Author: arnaudbore

scilpy/image/operations.py

@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 
 """
-Utility operations provided for scil_image_math.py and scil_connectivity_math.py
+Utility operations provided for scil_image_math.py
+and scil_connectivity_math.py
 They basically act as wrappers around numpy to avoid installing MRtrix/FSL
 to apply simple operations on nibabel images or numpy arrays.
 """
@@ -54,7 +55,7 @@ def get_image_ops():
     """Get a dictionary of all functions relating to image operations"""
     image_ops = get_array_ops()
     image_ops.update(OrderedDict([
-        ('concatenate', concat),
+        ('concatenate', concatenate),
         ('dilation', dilation),
         ('erosion', erosion),
         ('closing', closing),
@@ -83,6 +84,13 @@ def _validate_imgs(*imgs):
             raise ValueError('Not all inputs have the same shape!')
 
 
+def _validate_imgs_concat(*imgs):
+    """Make sure that all inputs are images."""
+    for img in imgs:
+        if not isinstance(img, nib.Nifti1Image):
+            raise ValueError('Inputs are not all images')
+
+
 def _validate_length(input_list, length, at_least=False):
     """Make sure the the input list has the right number of arguments
     (length)."""
@@ -499,20 +507,30 @@ def invert(input_list, ref_img):
     return output_data
 
 
-def concat(input_list, ref_img):
+def concatenate(input_list, ref_img):
     """
-    concat: IMGs
-        Concatenate a list of 3D images into a single 4D image.
+    concatenate: IMGs
+        Concatenate a list of 3D and 4D images into a single 4D image.
     """
-    _validate_imgs(*input_list, ref_img)
-    if len(input_list[0].header.get_data_shape()) != 3:
-        raise ValueError('Concatenate require 3D arrays.')
+
+    _validate_imgs_concat(*input_list, ref_img)
+    if len(input_list[0].header.get_data_shape()) > 4:
+        raise ValueError('Concatenate require 3D or 4D arrays.')
 
     input_data = []
     for img in input_list:
+
         data = img.get_fdata(dtype=np.float64)
-        input_data.append(data)
+
+        if len(img.header.get_data_shape()) == 4:
+            data = np.rollaxis(data, 3)
+            for i in range(0, len(data)):
+                input_data.append(data[i])
+        else:
+            input_data.append(data)
+
         img.uncache()
+
     return np.rollaxis(np.stack(input_data), axis=0, start=4)
 
 

scripts/scil_image_math.py

@@ -107,6 +107,15 @@ def main():
             found_ref = True
             break
 
+    # If there's a 4D image, replace the previous 3D image with
+    #  this one for reference
+    for input_arg in args.in_images:
+        if not is_float(input_arg):
+            ref_img = nib.load(input_arg)
+            if len(ref_img.shape) == 4:
+                mask = np.zeros(ref_img.shape)
+                break
+
     if not found_ref:
         raise ValueError('Requires at least one nifti image.')
 
@@ -137,7 +146,10 @@ def main():
 
         if isinstance(img, nib.Nifti1Image):
             data = img.get_fdata(dtype=np.float64)
-            mask[data > 0] = 1
+            if data.ndim == 4:
+                mask[np.sum(data, axis=3).astype(bool) > 0] = 1
+            else:
+                mask[data > 0] = 1
             img.uncache()
         input_img.append(img)
 

scripts/tests/test_image_math.py

@@ -45,7 +45,7 @@ def test_execution_low_mult(script_runner):
     assert ret.success
 
 
-def test_execution_concat(script_runner):
+def test_execution_concatenate(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_img_1 = os.path.join(get_home(), 'atlas', 'ids', '10.nii.gz')
     in_img_2 = os.path.join(get_home(), 'atlas', 'ids', '11.nii.gz')
@@ -57,3 +57,15 @@ def test_execution_concat(script_runner):
                             in_img_1, in_img_2, in_img_3, in_img_4, in_img_5,
                             in_img_6, 'concat_ids.nii.gz')
     assert ret.success
+
+
+def test_execution_concatenate_4D(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_img_1 = os.path.join(get_home(), 'atlas', 'ids', '10.nii.gz')
+    in_img_2 = os.path.join(get_home(), 'atlas', 'ids', '8_10.nii.gz')
+    in_img_3 = os.path.join(get_home(), 'atlas', 'ids', '12.nii.gz')
+    in_img_4 = os.path.join(get_home(), 'atlas', 'ids', '8_10.nii.gz')
+    ret = script_runner.run('scil_image_math.py', 'concatenate',
+                            in_img_1, in_img_2, in_img_3, in_img_4,
+                            'concat_ids_4d.nii.gz')
+    assert ret.success