nabu 2024.1.0rc4__tar.gz → 2024.1.2__tar.gz

{nabu-2024.1.0rc4/nabu.egg-info → nabu-2024.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.0rc4
+Version: 2024.1.2
 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>

{nabu-2024.1.0rc4 → nabu-2024.1.2}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.0-rc4"
+__version__ = "2024.1.2"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.1.0rc4 → nabu-2024.1.2}/nabu/app/cast_volume.py

@@ -228,11 +228,20 @@ def main(argv=None):
 
     # get rescale_min_percentile and rescale_min_percentile
     rescale_min_percentile = options.rescale_min_percentile
+
+    def clean_percentiles_str(percentile):
+        # remove ' char
+        percentile = percentile.rstrip("'").lstrip("'")
+        # remove " char
+        percentile = percentile.rstrip('"').lstrip('"')
+        # remove % char
+        return percentile.rstrip("%")
+
     if isinstance(rescale_min_percentile, str):
-        rescale_min_percentile = float(rescale_min_percentile.rstrip("%"))
+        rescale_min_percentile = float(clean_percentiles_str(rescale_min_percentile))
     rescale_max_percentile = options.rescale_max_percentile
     if isinstance(rescale_min_percentile, str):
-        rescale_max_percentile = float(rescale_max_percentile.rstrip("%"))
+        rescale_max_percentile = float(clean_percentiles_str(rescale_max_percentile))
     assert rescale_min_percentile is not None, "rescale_min_percentile should be an int"
     assert rescale_max_percentile is not None, "rescale_max_percentile should be an int"
 

{nabu-2024.1.0rc4 → nabu-2024.1.2}/nabu/app/multicor.py

@@ -60,12 +60,12 @@ def main():
     cors = get_user_cors(args["cor"])
 
     all_recs = []
+    rec_instance = pipeline.reconstruction
 
     for cor in cors:
         # Re-configure with new CoR
         pipeline.processing_options["reconstruction"]["rotation_axis_position"] = cor
         pipeline.processing_options["save"]["file_prefix"] = file_prefix + "_%.03f" % cor
-        pipeline.reconstruction.reset_rot_center(cor)
         pipeline._init_writer(create_subfolder=False, single_output_file_initialized=False)
 
         # Get sinogram into contiguous array
@@ -73,8 +73,30 @@ def main():
         # For now: transfer to host... not optimal
         sino = pipeline._d_radios[:, pipeline._d_radios.shape[1] // 2, :].get()  # pylint: disable=E1136
 
+        if pipeline.process_config.do_halftomo:
+            # re-initialize FBP object, because in half-tomography the output slice size is a function of CoR
+            options = pipeline.processing_options["reconstruction"]
+            rec_instance = pipeline.FBPClass(
+                sino.shape,
+                angles=options["angles"],
+                rot_center=cor,
+                filter_name=options["fbp_filter_type"] or "none",
+                halftomo=options["enable_halftomo"],
+                # slice_roi=self.process_config.rec_roi,
+                padding_mode=options["padding_type"],
+                extra_options={
+                    "scale_factor": 1.0 / options["voxel_size_cm"][0],
+                    "axis_correction": options["axis_correction"],
+                    "centered_axis": options["centered_axis"],
+                    "clip_outer_circle": options["clip_outer_circle"],
+                    "filter_cutoff": options["fbp_filter_cutoff"],
+                },
+            )
+        else:
+            pipeline.reconstruction.reset_rot_center(cor)
+
         # Run reconstruction
-        rec = pipeline.reconstruction.fbp(sino)
+        rec = rec_instance.fbp(sino)
         # if return_all_recs:
         # all_recs.append(rec)
         rec_3D = view_as_images_stack(rec)  # writer wants 3D data

{nabu-2024.1.0rc4 → nabu-2024.1.2}/nabu/io/cast_volume.py

@@ -74,7 +74,7 @@ def get_default_output_volume(
                 volume_basename=input_volume.get_volume_basename(),
             )
         else:
-            raise NotImplementedError
+            raise NotImplementedError(f"output volume format {output_type} is not handled")
     elif isinstance(input_volume, (HDF5Volume, MultiTIFFVolume)):
         if output_type == "hdf5":
             data_file_parent_path, data_file_name = os.path.split(input_volume.data_url.file_path())
@@ -121,9 +121,9 @@ def get_default_output_volume(
                 )
             )
         else:
-            raise NotImplementedError
+            raise NotImplementedError(f"output volume format {output_type} is not handled")
     else:
-        raise NotImplementedError
+        raise NotImplementedError(f"input volume format {input_volume} is not handled")
 
 
 def cast_volume(
@@ -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-2024.1.2}/nabu/io/utils.py

@@ -201,7 +201,7 @@ class EntryReader(_BaseReader):
     """Context manager used to read a bliss node"""
 
     def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
+        self._file_handler = HDF5File(self._url.file_path(), mode="r")
         if self._url.data_path() == "":
             entry = self._file_handler
         else:
@@ -215,7 +215,7 @@ class DatasetReader(_BaseReader):
     """Context manager used to read a bliss node"""
 
     def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
+        self._file_handler = HDF5File(self._url.file_path(), mode="r")
         entry = self._file_handler[self._url.data_path()]
         if not isinstance(entry, h5py.Dataset):
             raise ValueError("Data path ({}) should point to a dataset (h5py.Dataset)".format(self._url.path()))

{nabu-2024.1.0rc4 → nabu-2024.1.2}/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-2024.1.2}/nabu/stitching/tests/test_z_stitching.py

@@ -726,7 +726,6 @@ def test_get_overlap_areas():
 
 def test_frame_flip(tmp_path):
     """check it with some NXtomo fliped"""
-    pytest.skip(reason="Broken test")
     ref_frame_width = 280
     n_proj = 10
     raw_frame_width = 100

{nabu-2024.1.0rc4 → nabu-2024.1.2}/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,
@@ -1256,7 +1258,7 @@ class PreProcessZStitcher(ZStitcher):
 
         output_dtype = get_output_data_type()
         # append frames ("instrument/detactor/data" dataset)
-        with HDF5File(filename=self.configuration.output_file_path, mode="a") as h5f:
+        with HDF5File(self.configuration.output_file_path, mode="a") as h5f:
             # note: nx_tomo.save already handles the possible overwrite conflict by removing
             # self.configuration.output_file_path or raising an error
 
@@ -1832,7 +1834,7 @@ class PostProcessZStitcher(ZStitcher):
         def __enter__(self):
             # handle the specific case of HDF5. Goal: avoid getting the full stitched volume in memory
             if isinstance(self._volume, HDF5Volume):
-                self.__file_handler = HDF5File(filename=self._volume.data_url.file_path(), mode="a")
+                self.__file_handler = HDF5File(self._volume.data_url.file_path(), mode="a")
                 # if need to delete an existing dataset
                 if self._volume.overwrite and self._volume.data_path in self.__file_handler:
                     try:
@@ -1900,7 +1902,7 @@ class PostProcessZStitcher(ZStitcher):
                     if volume.data is not None:
                         data = volume.data
                     elif isinstance(volume, HDF5Volume):
-                        file_handler = HDF5File(filename=volume.data_url.file_path(), mode="r")
+                        file_handler = HDF5File(volume.data_url.file_path(), mode="r")
                         dataset = file_handler[volume.data_url.data_path()]
                         data = dataset
                         self.__file_handlers.append(file_handler)

{nabu-2024.1.0rc4 → nabu-2024.1.2/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.0rc4
+Version: 2024.1.2
 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>

{nabu-2024.1.0rc4 → nabu-2024.1.2}/nabu.egg-info/requires.txt

@@ -2,7 +2,7 @@ numpy>1.9.0
 scipy
 h5py>=3.0
 silx>=0.15.0
-tomoscan>=2.0.0a7
+tomoscan>=2.0.4
 psutil
 pytest
 tifffile

{nabu-2024.1.0rc4 → nabu-2024.1.2}/pyproject.toml

@@ -53,7 +53,7 @@ dependencies = [
     "scipy",
     "h5py>=3.0",
     "silx >= 0.15.0",
-    "tomoscan >= 2.0.0a7",
+    "tomoscan >= 2.0.4",
     "psutil",
     "pytest",
     "tifffile",