macapype 0.6__tar.gz → 0.7__tar.gz

macapype-0.7/LICENCE.txt

@@ -0,0 +1,7 @@
+Copyright 2021 Macatools
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

{macapype-0.6 → macapype-0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: macapype
-Version: 0.6
+Version: 0.7
 Summary: Pipeline for anatomic processing for macaque 
 Author: Macatools team
 Maintainer: Macapype developers
@@ -55,14 +55,14 @@ python setup.py develop
 
 # Docker image
 ```shell
-docker pull macatools/macapype/latest
+docker pull macatools/macapype:latest
 ```
 
 # Documentation
 
 https://macatools.github.io/macapype/
 
-# Related to project:
+# External documentation related to project
 
 [A guide for PNH MRI processing](https://github.com/PRIME-RE/prime-re.github.io/wiki), and in particular, the session on [structural MRI processing](https://github.com/PRIME-RE/prime-re.github.io/wiki/Structural-processing)
 
@@ -73,3 +73,7 @@ https://macatools.github.io/macapype/
 
 The macapype_users can be be found [here](https://framateam.org/signup_user_complete/?id=ebtxf45nmiyqmkm8e6oh9qjsoe) (requires a framateam/framagit account, but should be accessible with a github or bitbucket account)
 
+
+# Contribution to project
+
+Are you willing to contribute to the project? See the instructions in [CONTRIBUTING.md](https://github.com/macatools/macapype/blob/master/CONTRIBUTING.md)

{macapype-0.6 → macapype-0.7}/README.md

@@ -16,14 +16,14 @@ python setup.py develop
 
 # Docker image
 ```shell
-docker pull macatools/macapype/latest
+docker pull macatools/macapype:latest
 ```
 
 # Documentation
 
 https://macatools.github.io/macapype/
 
-# Related to project:
+# External documentation related to project
 
 [A guide for PNH MRI processing](https://github.com/PRIME-RE/prime-re.github.io/wiki), and in particular, the session on [structural MRI processing](https://github.com/PRIME-RE/prime-re.github.io/wiki/Structural-processing)
 
@@ -34,3 +34,7 @@ https://macatools.github.io/macapype/
 
 The macapype_users can be be found [here](https://framateam.org/signup_user_complete/?id=ebtxf45nmiyqmkm8e6oh9qjsoe) (requires a framateam/framagit account, but should be accessible with a github or bitbucket account)
 
+
+# Contribution to project
+
+Are you willing to contribute to the project? See the instructions in [CONTRIBUTING.md](https://github.com/macatools/macapype/blob/master/CONTRIBUTING.md)

{macapype-0.6 → macapype-0.7}/docs/conf.py

@@ -129,7 +129,7 @@ html_theme_options = {
         #("Github", "https://github.com/macatools/macapype", True),
     #]
     'navbar_links': [
-        ("Github", "https://github.com/davidmeunier79/macapype", True),
+        ("Github", "https://github.com/macatools/macapype", True),
     ]
     }
 

macapype-0.7/macapype/_version.py

@@ -0,0 +1 @@
+__version__ = '0.7'

{macapype-0.6 → macapype-0.7}/macapype/bash/IterREGBET.sh

@@ -278,11 +278,13 @@ for ((i = 1 ; i  <= $NITER ; i++)); do
   
   # Extra whole-head non-linear registration, if wanted
   if [[ -n $REF_WHOLE ]] && [[ $i == $NITER ]]; then
-    echo "FNIRT..."
+    echo "FNIRT..." 1>&2
     "${FSLPREFIX}fnirt" --in=$IN_WHOLE --ref=$REF_WHOLE --aff=$I2R_XFM --iout=${WARP[WH_OUT]} --cout=${WARP[WH_WARP]} # compute warp
-    echo "Inverting warp..."
+    #"${FSLPREFIX}fnirt" --in=$IN_WHOLE --ref=$REF_WHOLE --aff=$I2R_XFM --iout=${WARP[WH_OUT]} --cout=${WARP[WH_WARP]} --miter=5,3 --subsamp=4,2 --infwhm=6,4 --reffwhm=4,2 --estint=false --applyrefmask=false --applyinmask=false # compute warp
+    #"${FSLPREFIX}fnirt" --in=$IN_WHOLE --ref=$REF_WHOLE --aff=$I2R_XFM --iout=${WARP[WH_OUT]} --cout=${WARP[WH_WARP]} --miter=1 --subsamp=4 --infwhm=6 --reffwhm=4 --estint=false --applyrefmask=false --applyinmask=false # compute warp
+    echo "Inverting warp..." 1>&2
     "${FSLPREFIX}invwarp" -r $IN_WHOLE -w ${WARP[WH_WARP]} -o ${WARP[WH_INVWARP]}
-    echo "Applying inverse warp..."
+    echo "Applying inverse warp..." 1>&2
     "${FSLPREFIX}applywarp" --ref=$IN_WHOLE --in=${TMP[REF_MASK]} --out=$IN_OUT_MASK --warp=${WARP[WH_INVWARP]} --interp=nn
   else
     "${FSLPREFIX}flirt" -in ${TMP[REF_MASK]} -ref $IN_WHOLE -out $IN_OUT_MASK -interp nearestneighbour -applyxfm -init $R2I_XFM # move brain mask to in_file

{macapype-0.6 → macapype-0.7}/macapype/nodes/correct_bias.py

@@ -258,4 +258,4 @@ def itk_debias(img_file):
     mask_img_file = os.path.abspath(fname + "_mask" + ext)
     sitk.WriteImage(input_image_mask, mask_img_file)
 
-    return cor_img_file, bias_img_file
+    return cor_img_file, bias_img_file, mask_img_file

{macapype-0.6 → macapype-0.7}/macapype/nodes/prepare.py

@@ -273,7 +273,7 @@ class CropVolume(CommandLine):
 
 ###############################################################################
 # Equivalent of flirt_average in FSL
-def average_align(list_img, reorient=False):
+def average_align(list_img, reorient=False, max_index=None):
 
     import os
     import nibabel as nib
@@ -299,7 +299,16 @@ def average_align(list_img, reorient=False):
             data_0_shape = data_0.shape
             list_data = [data_0]
 
-            for i, img in enumerate(list_img[1:]):
+            if max_index is not None:
+                assert max_index < len(list_img), f"Error with {max_index=}"
+
+            for i, img in enumerate(list_img[1:], 1):
+
+                if max_index is not None:
+                    if i > max_index:
+                        print(f"Iter {i=} higher than {max_index=}")
+                        continue
+
                 data_orig_shape = nib.load(img).get_fdata().shape
                 if data_orig_shape != data_0_shape:
                     print(f"**** Warning , original image shape \

{macapype-0.6 → macapype-0.7}/macapype/nodes/register.py

@@ -221,6 +221,12 @@ class IterREGBETOutputSpec(TraitedSpec):
             exists=True,
             desc="inv_transfo_file")
 
+    nonlin_warp_file = File(
+            desc="nonlin_warp_file")
+
+    nonlin_invwarp_file = File(
+            desc="nonlin_invwarp_file")
+
 
 class IterREGBET(CommandLine):
     """
@@ -334,8 +340,16 @@ class IterREGBET(CommandLine):
             outfile = self._gen_outfilename()
 
         outputs["warp_file"] = os.path.abspath(outfile + ".nii.gz")
+
         outputs["transfo_file"] = os.path.abspath(outfile + ".xfm")
         outputs["inv_transfo_file"] = os.path.abspath(outfile + "_inverse.xfm")
+
+        if isdefined(self.inputs.refw_file) and self.inputs.k is True:
+            outputs["nonlin_warp_file"] = \
+                os.path.abspath(outfile + "_Warp.nii.gz")
+            outputs["nonlin_invwarp_file"] = \
+                os.path.abspath(outfile + "_InverseWarp.nii.gz")
+
         return outputs
 
 

{macapype-0.6 → macapype-0.7}/macapype/nodes/segment.py

@@ -248,15 +248,16 @@ def merge_imgs(list_img_files):
             path, fname, ext = split_f(img_file)
             img = nib.load(img_file)
             img_data = img.get_fdata()
-            new_img_data = np.zeros(shape=img_data.shape)
-            new_img_data[img_data != 0] += img_data[img_data != 0]
+            new_img_data = np.zeros(shape=img_data.shape, dtype=np.int32)
+            new_img_data[img_data != 0] = 1
 
         else:
             img_data = nib.load(img_file).get_fdata()
+
             assert img_data.shape == new_img_data.shape, \
                 "Error, shapes {} != {}".format(img_data.shape,
                                                 new_img_data.shape)
-            new_img_data[img_data != 0] += img_data[img_data != 0]
+            new_img_data[img_data != 0] = 1
 
     # creating indexed_mask
     merged_img = nib.Nifti1Image(dataobj=new_img_data,

{macapype-0.6 → macapype-0.7}/macapype/nodes/surface.py

@@ -4,20 +4,24 @@ from nipype.interfaces.base import (
 from nipype.interfaces.afni.base import AFNICommandBase
 
 
+def getLargestCC(segmentation):
+
+    from skimage.measure import label
+    import numpy as np
+
+    labels = label(segmentation)
+    assert labels.max() != 0  # assume at least 1 CC
+    largestCC = labels == np.argmax(np.bincount(labels.flat)[1:])+1
+    return largestCC, labels
+
+
 def keep_gcc(nii_file):
     import os
     import nibabel as nib
     import numpy as np
     from nipype.utils.filemanip import split_filename as split_f
 
-    def getLargestCC(segmentation):
-
-        from skimage.measure import label
-
-        labels = label(segmentation)
-        assert labels.max() != 0  # assume at least 1 CC
-        largestCC = labels == np.argmax(np.bincount(labels.flat)[1:])+1
-        return largestCC, labels
+    from macapype.nodes.surface import getLargestCC
 
     # nibabel (nifti -> np.array)
     img = nib.load(nii_file)
@@ -50,6 +54,44 @@ def keep_gcc(nii_file):
     return gcc_nii_file
 
 
+def keep_gcc_by_index(nii_file):
+    import os
+    import nibabel as nib
+    import numpy as np
+    from nipype.utils.filemanip import split_filename as split_f
+
+    from macapype.nodes.surface import getLargestCC
+
+    # nibabel (nifti -> np.array)
+    img = nib.load(nii_file)
+    data = img.get_fdata().astype(np.int16)
+
+    path, fname, ext = split_f(nii_file)
+
+    print(np.unique(data))
+
+    new_data = np.zeros(data.shape, data.dtype)
+
+    for index in np.unique(data)[1:]:
+        data_data_bin_index = np.zeros(data.shape, data.dtype)
+        data_data_bin_index[data == index] = 1
+
+        if np.sum(data_data_bin_index):
+            gcc_index_data, _ = getLargestCC(data_data_bin_index)
+            new_data[gcc_index_data] = index
+
+    # nibabel (np.array -> nifti)
+    new_img = nib.Nifti1Image(dataobj=new_data,
+                              header=img.header,
+                              affine=img.affine)
+
+    gcc_nii_file = os.path.abspath(fname + "_gcc" + ext)
+
+    nib.save(new_img, gcc_nii_file)
+
+    return gcc_nii_file
+
+
 def merge_tissues(dseg_file, keep_indexes):
 
     import os