nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.1__py3-none-any.whl

nabu/__init__.py

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

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/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/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.dist-info → nabu-2024.1.1.dist-info}/METADATA

@@ -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>