nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.2__py3-none-any.whl

nabu/__init__.py

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

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/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/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/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/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/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/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.dist-info → nabu-2024.1.2.dist-info}/METADATA

@@ -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>
@@ -53,7 +53,7 @@ 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: tomoscan >=2.0.4
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2024.1.0rc4.dist-info → nabu-2024.1.2.dist-info}/RECORD

@@ -1,14 +1,14 @@
 doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=VaZQ2L3-u3o0BhoSKKPN1P8e_Eo3k46aSuDjgmxLFcc,274
+nabu/__init__.py,sha256=ZAej-8X8A_uoviFokuukhi8jyzI2YRAj0-zkdCR3LaI,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=qqtGgkIhpOpXhgeoXlqCb91Rx-JlI4ALaDF6nt8YRRk,13298
 nabu/utils.py,sha256=1OKKhQ6-t7OOwTLQkTJuK5Hk9lb7hkEZrDtTdcmvD4c,24164
 nabu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/app/bootstrap.py,sha256=UQZzCBKtSXtQp5U0aXtlUhbjbwzgILTI4zD4zVffhBI,3246
 nabu/app/bootstrap_stitching.py,sha256=Inr0_zRAtyeMTK1BKxGqoDf-Na0O33CICmQJYja06ug,2148
-nabu/app/cast_volume.py,sha256=60mSXKivRMbK1TA8gsQROX2gmzCunCZG4TVP15t96yA,10928
+nabu/app/cast_volume.py,sha256=oObZVX-UbhsQ-JbNqpG1SdOSeJwIBrALYsJ9PubPWXc,11217
 nabu/app/cli_configs.py,sha256=FBh9bG80oY0fwfOntmgqgumS5i120_r60tCsj_mcdvE,22109
 nabu/app/compare_volumes.py,sha256=Mu5O4uP-ANo-el-fE5PLvEq42BTk5FkrscaFRyQZdis,3341
 nabu/app/composite_cor.py,sha256=N0Q7dxak7GktcuwxtwQ0PdZcmCS5CboChlxa2UCLMIA,5132
@@ -19,7 +19,7 @@ nabu/app/diag_to_rot.py,sha256=86lqINSN4SoQ0Eqf0fGYCw-eAhBHm8ds7TDWtLNE6Cg,17111
 nabu/app/double_flatfield.py,sha256=zm9oHWR_QgAV2B3SeNWwgxpJtBsnnWUW4O2lCn5Hjbc,5450
 nabu/app/generate_header.py,sha256=Voo-FAvwS_mU5gtDxyqpZnSpP_mlMSfd_6bEtgdi_tg,8919
 nabu/app/histogram.py,sha256=gyLXKwFrU5WPQMkM1k8OdpIXSwGEEKC-f8RcTHKOho4,7930
-nabu/app/multicor.py,sha256=7Y-V6IH0L9BBoPa1pW9hbY3CsBvJtABgwRQSwd5dMD8,2996
+nabu/app/multicor.py,sha256=h2ykS6Vg3S88E_pZOQu_s7F1VYGv-q7k1nfqxf2IdOM,4055
 nabu/app/nx_z_splitter.py,sha256=p54jR-PAAw-AkGolM9fZE5lM2vbNLspCNCy5zBnJNP4,4976
 nabu/app/parse_reconstruction_log.py,sha256=9eiJftCkyNvtZmTDjeOuKgu3a9Fe4KzJcfcI_ZdDlUM,4586
 nabu/app/prepare_weights_double.py,sha256=5TkhTwNbvgeG8jlDLCwlkeOV_YMINySwdpmjaTM6pbk,5495
@@ -76,12 +76,12 @@ nabu/estimation/tests/test_focus.py,sha256=deaVGbIFSzHDAReoeAy-1HLsnKWpJQsC2SL9W
 nabu/estimation/tests/test_tilt.py,sha256=PN4tnV3-XU2nNA608kQShaHugWn_-wbHzWCTnLIaCTk,1658
 nabu/estimation/tests/test_translation.py,sha256=RkOnCYgk9DZGKlIka1snqTv4wbIz_nG7-EHAxnBHsJU,2999
 nabu/io/__init__.py,sha256=Mx0HRIENk0dJbN3b9tzPZhiOnPMxBItgVNQn_QLLrlI,176
-nabu/io/cast_volume.py,sha256=KhwS8RKl17s39hJSSHnKVMIDMikVWYPYTomvQJgKBP8,15196
+nabu/io/cast_volume.py,sha256=k2EjcWwEjR30VAqm6XK_5ofoJXlAYtf4B2hCafnCVx4,15638
 nabu/io/detector_distortion.py,sha256=Or4icugi0fGRKWIG0I9hCuR1UZA5Cel25ZGY7cR2j4I,11744
 nabu/io/reader.py,sha256=1DlUYObfOBEGYJHEqyw1Mb2uQ_b_Z7-FFqMWS-4tIB0,23083
 nabu/io/reader_helical.py,sha256=_6vZBH-US_VT7oOGJUtYXqPwFws7xZKcmdOthpwvlIQ,4477
 nabu/io/tiffwriter_zmm.py,sha256=ykaSFqdbYhGNxdBrJRT_rxihx5wj9G8qMQMI1e07fNk,3838
-nabu/io/utils.py,sha256=EcaAdjD09h_6dbVX2Bl3xGhK83hXBslixcJ4zn5kfLM,9241
+nabu/io/utils.py,sha256=pFRULSlmGzJnzBbeSNKRhnKbBPbV0XaeUsxnWmnMtR4,9223
 nabu/io/writer.py,sha256=cWKY7RcNUztOs1ktzLP2G087fLvq4yNMNdvvBdnoOSk,31417
 nabu/io/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/io/tests/test_cast_volume.py,sha256=3zd_aGhMeMPkjg1I3Kq4oKltxwVloizXKgaDV8g_F7Q,10391
@@ -265,14 +265,14 @@ nabu/resources/tests/test_nxflatfield.py,sha256=wLcBYpeD1UHGbimRrisGzgS9oVnQ8nNz
 nabu/resources/tests/test_units.py,sha256=F2jFTck-1UwYET1MwTtX6ntzYUosfwOJkugSencGgz8,2155
 nabu/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/stitching/alignment.py,sha256=MSj-6npGfUnD3C5R5rqKwTogVRUDPmJuEZkPG9hMiUY,6752
-nabu/stitching/config.py,sha256=sFGcrs05KA5HH4auIU1gONtM2d2YCAjmibHxdwet_ww,51360
+nabu/stitching/config.py,sha256=t7mkRrkdHKMz0x-lg0f5-IOAO829A6BvKH8WUAuSAps,51333
 nabu/stitching/definitions.py,sha256=RyqzZY3KLwN4j0SkOFA-T1aicPbO2jBrqfWdz-1djxk,130
 nabu/stitching/frame_composition.py,sha256=OGM9cLrLfEP5_hvhDbNq_zr2wdMeAuTTNlVqZk-qVBU,5889
 nabu/stitching/overlap.py,sha256=eXAKsILS5jwqFY62JhDijeNW8H50rP-yjdUUGqjj0aY,15700
 nabu/stitching/sample_normalization.py,sha256=_radin_wxnuD3MMmZNAOKA__aPa2z3ss4TFbZeocpXc,2069
 nabu/stitching/slurm_utils.py,sha256=sZ-VQPh_YlJ1Lkh7ap8qxII0rBpZryMyoxE5Xn557t8,8906
 nabu/stitching/utils.py,sha256=kMn2JEMDhcBQMweSlM0rUd-037H7iNUURTFMhXOTzC8,23651
-nabu/stitching/z_stitching.py,sha256=yI0jmmP3y_0VrbzYUBXT9x3F0KIBwNOAuTdQ3nlCdsM,103356
+nabu/stitching/z_stitching.py,sha256=RRrLUDiOrImj1wvun13RkEC9tYL3WvbCNzS66iSKMgg,103400
 nabu/stitching/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/stitching/tests/test_alignment.py,sha256=MACak1ILOr8nRKeT0mWfMd-ZvhCl3SWjjcp6GjRbITc,2735
 nabu/stitching/tests/test_config.py,sha256=ttWuVB9Y_MM3_wGdKbcbYi_PG3vN87cL7o5zKsMzn9g,8490
@@ -281,16 +281,16 @@ nabu/stitching/tests/test_overlap.py,sha256=vfZuK32pclWL0Hg8u5NH0JoxKO28qk3ObRMm
 nabu/stitching/tests/test_sample_normalization.py,sha256=E49E_Quv-Qon6qSuaH9ZBZLqq4TPuBl8RqgB18Rwjc0,1348
 nabu/stitching/tests/test_slurm_utils.py,sha256=bbhCQd06R3irGB4B9r79KKlf0AlBchI53N2ldsXoAQQ,4950
 nabu/stitching/tests/test_utils.py,sha256=CjV0vPvXEchJ5vo6o7hGQA-PsOOAyAamuQ6fiHKCQ9M,641
-nabu/stitching/tests/test_z_stitching.py,sha256=1bNvNkWDqV4mE5tgHBKqshDnoJtMPzUS2xCkf9qd2XM,42620
+nabu/stitching/tests/test_z_stitching.py,sha256=8gio27FTULOX7bzypmdaAyVwQiO-JOwgBL1e9FwZUN4,42582
 nabu/thirdparty/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/thirdparty/algotom_convert_sino.py,sha256=iZVRilvyqMyLTu8RKgbqDFUjObWW5X69rCARrnNizuI,13872
 nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtCl6G2NebJlbg,4500
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=VgXHr2tzTAAGZix5pwhFfbPxj4tt3yXBcjCPNQSLPAg,22810
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2024.1.0rc4.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.1.0rc4.dist-info/METADATA,sha256=YqG-9EJ_oEis_rU6GzT1c_4TtNLbovDQAloRyPVhlE0,5229
-nabu-2024.1.0rc4.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.1.0rc4.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.1.0rc4.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.1.0rc4.dist-info/RECORD,,
+nabu-2024.1.2.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.1.2.dist-info/METADATA,sha256=SNK5avox9pDHbu-OEbx204ASbhwoMmjSC3e5_9ilMFI,5224
+nabu-2024.1.2.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+nabu-2024.1.2.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.1.2.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.1.2.dist-info/RECORD,,