Merge pull request #204 from UKRIN-MAPS/rel/v0.6.5

rel/v0.6.5
UKRIN-MAPS · Feb 20, 2023 · a7126d0 · a7126d0
2 parents 4b24ab5 + cfcd84d
commit a7126d0
Show file tree

Hide file tree

Showing 22 changed files with 88 additions and 34 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,15 @@
+## [0.6.5] - 2023-02-17
+
+### Added
+* Number of downloads badge to readme
+
+### Changed
+* Lots of dependencies have been updated to their latest versions #203
+* Dependencies are now set to be compatible versions (~=) rather than greater than a specific version (>=) #203
+
+### Fixed
+* MTR outputs are now squeezed to remove bonus dimensions #202
+
 ## [0.6.4] - 2022-11-21
 
 ### Added

diff --git a/CITATION.cff b/CITATION.cff
@@ -17,7 +17,7 @@ authors:
   given-names: "Susan T"
   orcid: "https://orcid.org/0000-0003-0903-7507"
 title: "UKRIN Kidney Analysis Toolbox"
-version: 0.6.4
+version: 0.6.5
 doi: 10.5281/zenodo.4742470
-date-released: 2022-11-21
+date-released: 2023-02-17
 url: "https://github.com/UKRIN-MAPS/ukat"
diff --git a/README.md b/README.md
@@ -4,6 +4,7 @@
 ![Build and Test](https://github.com/UKRIN-MAPS/ukat/workflows/Build%20and%20Test/badge.svg?branch=master)
 [![codecov](https://codecov.io/gh/UKRIN-MAPS/ukat/branch/master/graph/badge.svg?token=QJ9DQONJBP)](https://codecov.io/gh/UKRIN-MAPS/ukat)
 [![PyPI version](https://badge.fury.io/py/ukat.svg)](https://badge.fury.io/py/ukat)
+[![Downloads](https://static.pepy.tech/badge/ukat)](https://pepy.tech/project/ukat)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![DOI](https://zenodo.org/badge/256993671.svg)](https://zenodo.org/badge/latestdoi/256993671)
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,12 +1,12 @@
-dipy>=1.2.0
-matplotlib>=3.1.3
-nibabel>=3.0.2
-notebook>=6.0.1
-numpy>=1.21.2
-pandas>=1.3.5
-renalsegmentor>=1.3.5
-scikit-image>=0.16.2
-scipy>=1.7.3
-scikit-learn>=1.0.2
-tabulate>=0.8.9
-tqdm>=4.48
+dipy~=1.6.0
+matplotlib~=3.7.0
+nibabel~=5.0.1
+notebook~=6.5.1
+numpy~=1.24.1
+pandas~=1.5.1
+renalsegmentor~=1.3.6
+scikit-image~=0.19.1
+scipy~=1.10.0
+scikit-learn~=1.2.1
+tabulate~=0.9.0
+tqdm~=4.64.1
diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@
 
 setup(
     name="ukat",
-    version="0.6.4",
+    version="0.6.5",
     description="UKRIN Kidney Analysis Toolbox",
     long_description=long_description,
     long_description_content_type="text/markdown",

diff --git a/ukat/mapping/b0.py b/ukat/mapping/b0.py
@@ -145,7 +145,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                     b0_nifti = nib.Nifti1Image(self.b0_map, affine=self.affine)
                     nib.save(b0_nifti, base_path + '_b0_map.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
                 elif result == 'phase0':

diff --git a/ukat/mapping/diffusion.py b/ukat/mapping/diffusion.py
@@ -255,7 +255,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                                                     affine=self.affine)
                     nib.save(adc_err_nifti, base_path + '_adc_err.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:
@@ -406,7 +406,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                     nib.save(color_fa_nifti, base_path +
                              '_color_fa_map.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:

diff --git a/ukat/mapping/mtr.py b/ukat/mapping/mtr.py
@@ -64,12 +64,12 @@ def __init__(self, pixel_array, affine, mask=None):
         else:
             self.mask = mask
         # The assumption is that MT_OFF comes first in `pixel_array`
-        self.mt_off = self.pixel_array[..., 0] * self.mask
+        self.mt_off = np.squeeze(self.pixel_array[..., 0] * self.mask)
         # The assumption is that MT_ON comes second in `pixel_array`
-        self.mt_on = self.pixel_array[..., 1] * self.mask
+        self.mt_on = np.squeeze(self.pixel_array[..., 1] * self.mask)
         # Magnetisation Transfer Ratio calculation
-        self.mtr_map = np.nan_to_num(((self.mt_off - self.mt_on) /
-                                     self.mt_off), posinf=0, neginf=0)
+        self.mtr_map = np.squeeze(np.nan_to_num(((self.mt_off - self.mt_on) /
+                                     self.mt_off), posinf=0, neginf=0))
 
     def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                  maps='all'):
@@ -94,18 +94,21 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
             for result in maps:
                 if result == 'mtr' or result == 'mtr_map':
                     mtr_nifti = nib.Nifti1Image(self.mtr_map,
-                                                affine=self.affine)
+                                                affine=self.affine,
+                                                dtype=float)
                     nib.save(mtr_nifti, base_path + '_mtr_map.nii.gz')
                 elif result == 'mt_on':
                     mt_on_nifti = nib.Nifti1Image(self.mt_on,
-                                                  affine=self.affine)
+                                                  affine=self.affine,
+                                                  dtype=float)
                     nib.save(mt_on_nifti, base_path + '_mt_on.nii.gz')
                 elif result == 'mt_off':
                     mt_off_nifti = nib.Nifti1Image(self.mt_off,
-                                                   affine=self.affine)
+                                                   affine=self.affine,
+                                                   dtype=float)
                     nib.save(mt_off_nifti, base_path + '_mt_off.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:

diff --git a/ukat/mapping/t1.py b/ukat/mapping/t1.py
@@ -344,7 +344,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                                                affine=self.affine)
                     nib.save(r1_nifti, base_path + '_r1_map.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:

diff --git a/ukat/mapping/t2.py b/ukat/mapping/t2.py
@@ -297,7 +297,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                                                affine=self.affine)
                     nib.save(r2_nifti, base_path + '_r2_map.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:

diff --git a/ukat/mapping/t2star.py b/ukat/mapping/t2star.py
@@ -318,7 +318,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                                                    affine=self.affine)
                     nib.save(r2star_nifti, base_path + '_r2star_map.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:

diff --git a/ukat/mapping/tests/test_b0.py b/ukat/mapping/tests/test_b0.py
@@ -91,6 +91,8 @@ def test_to_nifti(self):
         mapper = B0(self.correct_array, self.correct_echo_list,
                     self.affine, unwrap=False)
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/mapping/tests/test_diffusion.py b/ukat/mapping/tests/test_diffusion.py
@@ -146,6 +146,8 @@ def test_ukrin_b(self):
     def test_to_nifti(self):
         mapper = ADC(self.pixel_array, self.affine, self.bvals, self.mask)
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.
@@ -263,6 +265,8 @@ def test_to_nifti(self):
         mapper = DTI(self.pixel_array, self.affine, self.bvals, self.bvecs,
                      self.mask)
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/mapping/tests/test_mtr.py b/ukat/mapping/tests/test_mtr.py
@@ -64,6 +64,8 @@ def test_to_nifti(self):
         # Create a MTR map instance and test different export to NIFTI options.
         mapper = MTR(self.correct_array, self.affine)
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/mapping/tests/test_t1.py b/ukat/mapping/tests/test_t1.py
@@ -307,6 +307,8 @@ def test_to_nifti(self):
         signal_array = np.tile(self.correct_signal_three_param, (10, 10, 3, 1))
         mapper = T1(signal_array, self.t, self.affine, parameters=3)
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/mapping/tests/test_t2.py b/ukat/mapping/tests/test_t2.py
@@ -176,6 +176,8 @@ def test_to_nifti(self):
         signal_array = np.tile(self.correct_signal, (10, 10, 3, 1))
         mapper = T2(signal_array, self.t, self.affine)
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/mapping/tests/test_t2star.py b/ukat/mapping/tests/test_t2star.py
@@ -120,6 +120,8 @@ def test_to_nifti(self):
         signal_array = np.tile(self.correct_signal, (10, 10, 3, 1))
         mapper = T2Star(signal_array, self.t, self.affine, method='2p_exp')
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/qa/tests/test_snr.py b/ukat/qa/tests/test_snr.py
@@ -136,7 +136,11 @@ def test_different_clusters(self):
     def test_to_nifti(self):
         data, affine = fetch.t2w_volume_philips()
         isnr_obj = snr.Isnr(data, affine)
+
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
+
         isnr_obj.to_nifti('test_output', base_file_name='T2w')
         output_files = os.listdir('test_output')
         assert len(output_files) == 1
@@ -214,7 +218,11 @@ def test_real_data(self):
 
     def test_to_nifti(self):
         tsnr_obj = snr.Tsnr(self.data, self.affine)
+
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
+
         tsnr_obj.to_nifti('test_output', base_file_name='synthetic_data')
         output_files = os.listdir('test_output')
         assert len(output_files) == 1

diff --git a/ukat/segmentation/tests/test_whole_kidney.py b/ukat/segmentation/tests/test_whole_kidney.py
@@ -70,7 +70,10 @@ def test_save_volumes_csv(self):
                      '118.19352480602264',
                      '121.80702174282074']]
 
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
+
         self.segmentation.save_volumes_csv('test_output/volumes.csv')
         output_files = os.listdir('test_output')
 
@@ -86,6 +89,8 @@ def test_save_volumes_csv(self):
         shutil.rmtree('test_output')
 
     def test_to_nifti(self):
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
 
         # Check all is saved.

diff --git a/ukat/segmentation/whole_kidney.py b/ukat/segmentation/whole_kidney.py
@@ -183,19 +183,24 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
         if isinstance(maps, list):
             for result in maps:
                 if result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self._mask, self.affine)
+                    mask_nifti = nib.Nifti1Image(self.get_mask(),
+                                                 self.affine,
+                                                 dtype=np.uint16)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
                 elif result == 'left':
                     left_nifti = nib.Nifti1Image(self.get_left_kidney(),
-                                                 self.affine)
+                                                 self.affine,
+                                                 dtype=np.uint16)
                     nib.save(left_nifti, base_path + '_left_kidney.nii.gz')
                 elif result == 'right':
                     right_nifti = nib.Nifti1Image(self.get_right_kidney(),
-                                                  self.affine)
+                                                  self.affine,
+                                                  dtype=np.uint16)
                     nib.save(right_nifti, base_path + '_right_kidney.nii.gz')
                 elif result == 'individual':
                     ind_nifti = nib.Nifti1Image(self.get_kidneys(),
-                                                self.affine)
+                                                self.affine,
+                                                dtype=np.uint16)
                     nib.save(ind_nifti, base_path +
                              '_individual_kidneys.nii.gz')
         else:

diff --git a/ukat/vessels/phase_contrast.py b/ukat/vessels/phase_contrast.py
@@ -248,7 +248,7 @@ def to_nifti(self, output_directory=os.getcwd(), base_file_name='Output',
                     nib.save(velocity_nifti, base_path +
                              '_velocity_array.nii.gz')
                 elif result == 'mask':
-                    mask_nifti = nib.Nifti1Image(self.mask.astype(int),
+                    mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
                                                  affine=self.affine)
                     nib.save(mask_nifti, base_path + '_mask.nii.gz')
         else:

diff --git a/ukat/vessels/tests/test_phase_contrast.py b/ukat/vessels/tests/test_phase_contrast.py
@@ -134,6 +134,8 @@ def test_get_stats_table(self):
         assert number_columns == 7
 
     def test_to_csv(self):
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
         csv_path = os.path.join('test_output', "pc_test_output.csv")
         pc_obj = PhaseContrast(self.correct_signal, self.affine, self.mask)
@@ -161,7 +163,11 @@ def test_plot(self):
     def test_to_nifti(self):
         # Create a PC instance and test different export to NIFTI scenarios
         pc_obj = PhaseContrast(self.correct_signal, self.affine, self.mask)
+
+        if os.path.exists('test_output'):
+            shutil.rmtree('test_output')
         os.makedirs('test_output', exist_ok=True)
+
         # Check all is saved.
         pc_obj.to_nifti(output_directory='test_output',
                         base_file_name='pctest', maps='all')