Merge pull request dipy#3101 from skoudoro/fix-log-workflows

[BF] Uniformize cython version

dipy/workflows/io.py

@@ -434,7 +434,7 @@ class ConvertTensorsFlow(Workflow):
     def get_short_name(cls):
         return 'convert_tensors'
 
-    def run(self, tensor_files, from_format='dipy', to_format='mrtrix',
+    def run(self, tensor_files, from_format='mrtrix', to_format='dipy',
             out_dir='.', out_tensor='converted_tensor'):
         """Converts tensor representation between different formats.
 

dipy/workflows/reconst.py

@@ -218,7 +218,7 @@ def run(self, data_files, bvals_files, bvecs_files, small_delta, big_delta,
                 save_nifti(out_parng, n.astype(np.float32), affine)
 
             logging.info('MAPMRI saved in {0}'.
-                         format(os.path.dirname(out_dir)))
+                         format(os.path.abspath(out_dir)))
 
 
 class ReconstDtiFlow(Workflow):
@@ -404,7 +404,8 @@ def run(self, input_files, bvalues_files, bvectors_files, mask_files,
                 save_nifti(oevals, tenfit.evals.astype(np.float32), affine)
 
             if save_metrics:
-                logging.info('DTI metrics saved to')
+                msg = f'DTI metrics saved to {os.path.abspath(out_dir)}'
+                logging.info(msg)
                 for metric in save_metrics:
                     logging.info(self.last_generated_outputs["out_" + metric])
 
@@ -530,7 +531,8 @@ def run(self, input_files, bvalues_files, bvectors_files, mask_files,
                 peaks_to_niftis(peaks_dsi, oshm, opeaks_dir, opeaks_values,
                                 opeaks_indices, reshape_dirs=True)
 
-            logging.info('DSI metrics saved to {0}'.format(out_dir))
+            logging.info('DSI metrics saved to {0}'.
+                         format(os.path.abspath(out_dir)))
 
 
 class ReconstCSDFlow(Workflow):

doc/recipes.rst

@@ -25,29 +25,34 @@ answer it yourself and contribute to the documentation!
         save_tractogram(my_trk.streamlines, my_trk_file_path, 'same')
 
 
-.. dropdown:: How do I convert my Spherical Harmonics from DIPY to MRTRIX3?
+.. dropdown:: How do I convert my Spherical Harmonics from MRTRIX3 to DIPY?
    :animate: fade-in-slide-down
 
-   *Available only on master branch. See `this thread <https://github.com/dipy/dipy/discussions/2959#discussioncomment-7481675>`_ for more information.
+   *Available from DIPY 1.9.0+. See `this thread <https://github.com/dipy/dipy/discussions/2959#discussioncomment-7481675>`_ for more information.
 
    .. code-block:: Python
 
         from dipy.reconst.shm import convert_sh_descoteaux_tournier
         convert_sh_descoteaux_tournier(sh_coeffs)
 
-.. dropdown:: How do I convert my tensors from DIPY to FSL?
+.. dropdown:: How do I convert my tensors from FSL to DIPY  or MRTRIX3 to DIPY?
    :animate: fade-in-slide-down
 
-   *Available only on master branch
+   *Available with DIPY 1.9.0+
 
    .. code-block:: Python
 
         from dipy.reconst.utils import convert_tensors
         from dipy.io.image import load_nifti, save_nifti
 
         data, affine, img = load_nifti('my_data.nii.gz', return_img=True)
-        otensor = convert_tensors(data, 'dipy', 'fsl')
+        # convert from FSL to DIPY
+        otensor = convert_tensors(data, 'fsl', 'dipy')
         save_nifti(otensor, data, affine, image.header)
+        # convert from MRTRIX3 to DIPY
+        otensor = convert_tensors(data, 'mrtrix', 'dipy')
+        save_nifti(otensor, data, affine, image.header)
+
 
 
 .. include:: links_names.inc

pyproject.toml

@@ -3,7 +3,7 @@ name = "dipy"
 description = "Diffusion MRI Imaging in Python"
 license = {file = "LICENSE"}
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 authors = [{ name = "DIPY developers", email = "[email protected]" }]
 maintainers = [
     {name = "Eleftherios Garyfallidis", email="[email protected]"},
@@ -99,7 +99,7 @@ dev = [
     'setuptools>=67',
     'packaging>=21',
     'ninja',
-    'Cython>=0.29.32',
+    'Cython>=0.29.35',
     'numpy>=1.22',
     # Developer UI
     'spin>=0.5',

requirements.txt

@@ -1,5 +1,5 @@
 # Check against .travis.yml file and dipy/info.py
-cython>=0.29.24, !=0.29.29
+cython>=0.29.35, !=0.29.29
 numpy>=1.22.4
 scipy>=1.8.1
 nibabel>=4.0.0

requirements/build.txt

@@ -1,6 +1,6 @@
 meson-python>=0.13
 ninja
-Cython>=0.29.21
+Cython>=0.29.35
 packaging>=20.0
 wheel
 build