nabu 2024.1.0rc4__tar.gz → 2024.1.1__tar.gz

{nabu-2024.1.0rc4/nabu.egg-info → nabu-2024.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.0rc4
+Version: 2024.1.1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>
@@ -48,9 +48,29 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>1.9.0
+Requires-Dist: scipy
+Requires-Dist: h5py>=3.0
+Requires-Dist: silx>=0.15.0
+Requires-Dist: tomoscan>=2.0.0a7
+Requires-Dist: psutil
+Requires-Dist: pytest
+Requires-Dist: tifffile
 Provides-Extra: full
+Requires-Dist: scikit-image; extra == "full"
+Requires-Dist: PyWavelets; extra == "full"
+Requires-Dist: glymur; extra == "full"
+Requires-Dist: pycuda; extra == "full"
+Requires-Dist: scikit-cuda; extra == "full"
+Requires-Dist: pycudwt; extra == "full"
+Requires-Dist: sluurp>=0.3; extra == "full"
+Requires-Dist: pyvkfft; extra == "full"
 Provides-Extra: doc
-License-File: LICENSE
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cloud_sptheme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
 
 # Nabu
 

{nabu-2024.1.0rc4 → nabu-2024.1.1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.0-rc4"
+__version__ = "2024.1.1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.1.0rc4 → nabu-2024.1.1}/nabu/io/cast_volume.py

@@ -167,6 +167,12 @@ def cast_volume(
     if not isinstance(output_volume, VolumeBase):
         raise TypeError(f"output_volume is expected to be a {VolumeBase}. {type(output_volume)} provided")
 
+    try:
+        output_data_type = numpy.dtype(
+            output_data_type
+        )  # User friendly API in case user provides np.uint16 e.g. (see issue #482)
+    except Exception:
+        pass
     if not isinstance(output_data_type, numpy.dtype):
         raise TypeError(f"output_data_type is expected to be a {numpy.dtype}. {type(output_data_type)} provided")
 
@@ -326,7 +332,7 @@ def find_histogram(volume: VolumeBase, scan: Optional[TomoScanBase] = None) -> O
             )
 
 
-def _get_hst_saturations(hist, bins, rescale_min_percentile, rescale_max_percentile):
+def _get_hst_saturations(hist, bins, rescale_min_percentile: numpy.float32, rescale_max_percentile: numpy.float32):
     hist_cum = numpy.cumsum(hist)
     bin_index_min = numpy.searchsorted(hist_cum, numpy.percentile(hist_cum, rescale_min_percentile))
     bin_index_max = numpy.searchsorted(hist_cum, numpy.percentile(hist_cum, rescale_max_percentile))
@@ -360,4 +366,6 @@ def _min_max_from_histo(url: DataUrl, rescale_min_percentile: int, rescale_max_p
     else:
         bins = histogram[1]
         hist = histogram[0]
-        return _get_hst_saturations(hist, bins, rescale_min_percentile, rescale_max_percentile)
+        return _get_hst_saturations(
+            hist, bins, numpy.float32(rescale_min_percentile), numpy.float32(rescale_max_percentile)
+        )

{nabu-2024.1.0rc4 → nabu-2024.1.1}/nabu/stitching/config.py

@@ -710,12 +710,12 @@ class StitchingConfiguration:
                     "type": "optional",
                 },
                 SLURM_PREPROCESSING_COMMAND: {
-                    "default": "'/scisoft/tomotools_env/activate.sh stable'",
+                    "default": "",
                     "help": "python virtual environment to use",
                     "type": "optional",
                 },
                 SLURM_MODULES_TO_LOADS: {
-                    "default": "",
+                    "default": "tomotools/stable",
                     "help": "module to load",
                     "type": "optional",
                 },

{nabu-2024.1.0rc4 → nabu-2024.1.1}/nabu/stitching/z_stitching.py

@@ -1223,7 +1223,9 @@ class PreProcessZStitcher(ZStitcher):
 
         # first save the NXtomo entry without the frame
         # dicttonx will fail if the folder does not exists
-        os.makedirs(os.path.dirname(self.configuration.output_file_path), exist_ok=True)
+        dir_name = os.path.dirname(self.configuration.output_file_path)
+        if dir_name not in (None, ""):
+            os.makedirs(dir_name, exist_ok=True)
         nx_tomo.save(
             file_path=self.configuration.output_file_path,
             data_path=self.configuration.output_data_path,

{nabu-2024.1.0rc4 → nabu-2024.1.1/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.0rc4
+Version: 2024.1.1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>
@@ -48,9 +48,29 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>1.9.0
+Requires-Dist: scipy
+Requires-Dist: h5py>=3.0
+Requires-Dist: silx>=0.15.0
+Requires-Dist: tomoscan>=2.0.0a7
+Requires-Dist: psutil
+Requires-Dist: pytest
+Requires-Dist: tifffile
 Provides-Extra: full
+Requires-Dist: scikit-image; extra == "full"
+Requires-Dist: PyWavelets; extra == "full"
+Requires-Dist: glymur; extra == "full"
+Requires-Dist: pycuda; extra == "full"
+Requires-Dist: scikit-cuda; extra == "full"
+Requires-Dist: pycudwt; extra == "full"
+Requires-Dist: sluurp>=0.3; extra == "full"
+Requires-Dist: pyvkfft; extra == "full"
 Provides-Extra: doc
-License-File: LICENSE
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cloud_sptheme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
 
 # Nabu
 

{nabu-2024.1.0rc4 → nabu-2024.1.1}/nabu.egg-info/SOURCES.txt

@@ -40,7 +40,6 @@ nabu/app/shrink_dataset.py
 nabu/app/stitching.py
 nabu/app/utils.py
 nabu/app/validator.py
-nabu/app/tests/__init__.py
 nabu/app/tests/test_reduce_dark_flat.py
 nabu/cuda/__init__.py
 nabu/cuda/convolution.py

{nabu-2024.1.0rc4 → nabu-2024.1.1}/nabu.egg-info/top_level.txt

@@ -2,4 +2,3 @@ build
 dist
 doc
 nabu
-scripts