nabu 2023.1.0a1__py3-none-any.whl → 2023.1.0a2__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2023.1.0-alpha1"
+__version__ = "2023.1.0-alpha2"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/app/cast_volume.py

@@ -101,6 +101,11 @@ def main(argv=None):
 
     if os.path.exists(options.input_volume):
         volumes = guess_volumes(options.input_volume)
+
+        def is_not_histogram(vol_identifier):
+            return not (hasattr(vol_identifier, "data_path") and vol_identifier.data_path.endswith("histogram"))
+
+        volumes = tuple(filter(is_not_histogram, volumes))
         if len(volumes) == 0:
             _logger.error(f"no valid volume found in {options.input_volume}")
             exit(1)

nabu/io/cast_volume.py

@@ -276,7 +276,16 @@ def find_histogram(volume: VolumeBase, scan: Optional[TomoScanBase] = None) -> O
     elif isinstance(volume, HDF5Volume):
         histogram_file = volume.data_url.file_path()
         if volume.url is not None:
-            data_path = "/".join((volume.url.data_path(), "histogram/results/data"))
+            data_path = volume.url.data_path()
+            if data_path.endswith("reconstruction"):
+                data_path = "/".join(
+                    [
+                        *data_path.split("/")[:-1],
+                        "histogram/results/data",
+                    ]
+                )
+            else:
+                data_path = "/".join((volume.url.data_path(), "histogram/results/data"))
         else:
             # TODO: FIXME: in some case (if the users provides the full data_url and if the 'DATA_DATASET_NAME' is not used we
             # will endup with an invalid data_path. Hope this case will not happen. Anyway this is a case that we can't handle.)

nabu/pipeline/datadump.py

@@ -94,7 +94,7 @@ class DataDumpManager:
                     "processing_options": self.processing_options,  # slow!
                     "nabu_config": self.process_config.nabu_config,
                 },
-                "entry": getattr(self.dataset_info.dataset_scanner, "entry", None),
+                "entry": getattr(self.dataset_info.dataset_scanner, "entry", "entry"),
             },
         )
 

nabu/pipeline/fullfield/chunked.py

@@ -368,6 +368,10 @@ class ChunkedPipeline:
         # Use chunk_reader.files instead of process_config.projs_indices(subsampling=True), because
         # chunk_reader might read only a subset of the files (in "grouped mode")
         self._ff_options["projs_indices"] = list(self.chunk_reader.files_subsampled.keys())
+        if self._ff_options.get("normalize_srcurrent", False):
+            a_start_idx, a_end_idx = self.sub_region[0]
+            subs = self.process_config.subsampling_factor
+            self._ff_options["radios_srcurrent"] = self._ff_options["radios_srcurrent"][a_start_idx:a_end_idx:subs]
 
         distortion_correction = None
         if self._ff_options["do_flat_distortion"]:
@@ -588,7 +592,7 @@ class ChunkedPipeline:
             # "processing_options": self.processing_options,
             #
             "nabu_config": self.process_config.nabu_config,
-            "entry": getattr(self.dataset_info.dataset_scanner, "entry", None),
+            "entry": getattr(self.dataset_info.dataset_scanner, "entry", "entry"),
         }
         writer_extra_options = {
             "jpeg2000_compression_ratio": options["jpeg2000_compression_ratio"],

nabu/pipeline/helical/helical_reconstruction.py

@@ -409,11 +409,7 @@ class HelicalReconstructorRegridded:
         self.logger.info(f"Creating SpanStrategy object for helical in {duration} seconds")
         if self.dry_run:
             info_string = self._span_info.get_informative_string()
-            print(" SPAN_INFO informations ")
-            print(info_string)
-
-            info_string = self._span_info.get_informative_string()
-            print(" SPAN_INFO informations ")
+            print(" Informations about the doable vertical span")
             print(info_string)
             return
 

nabu/pipeline/helical/nabu_config.py

@@ -108,13 +108,13 @@ nabu_config["reconstruction"].update(
             "type": "optional",
         },
         "start_z": {
-            "default": "",
+            "default": "0",
             "help": "the first slice of the reconstructed range. Numbered going in the direction of the scan and starting with number zero for the first doable slice",
             "validator": slice_num_validator,
             "type": "optional",
         },
         "end_z": {
-            "default": "",
+            "default": "-1",
             "help": "the "
             "end"
             " slice of the reconstructed range. Numbered going in the direction of the scan and starting with number zero for the first doable slice",

nabu/pipeline/helical/span_strategy.py

@@ -26,7 +26,7 @@ class SpanStrategy:
         ----------
         z_pix_per_proj : array of floats
             an array of floats with one entry per projection, in pixel units. The values are the vertical displacements of the detector.
-            An increasing z means that the rotation axis is following the positive direction of the detector  vertical axis, which is pointing toward the ground.
+            An decreasing z means that the rotation axis is following the positive direction of the detector  vertical axis, which is pointing toward the ground.
             In the experimental setup, the vertical detector axis is pointing toward the ground. Moreover the values are offsetted so that the
             first value is zero. The offset value, in millimiters is z_offset_mm and it is the vertical position of the sample stage relatively
             to the center of the detector. A negative z_offset_mm means that the sample stage is below the detector for the first projection, and this is almost
@@ -186,9 +186,18 @@ class SpanStrategy:
 
     def get_informative_string(self):
         doable_span_v = self.get_doable_span()
+        if self.z_pix_per_proj[-1] > self.z_pix_per_proj[-1]:
+            direction = "ascending"
+        else:
+            direction = "descending"
+
         s = f"""
         Doable vertical span
         --------------------
+             The scan has been performed with an {direction} vertical translation of the rotation axis.
+              
+             The detector vertical axis is up side down.
+
              Detector reference system at iproj=0:
                 from vertical view height  ...   {doable_span_v.view_heights_minmax[0]}
                 up to  (included)     ...   {doable_span_v.view_heights_minmax[1]}
@@ -196,9 +205,7 @@ class SpanStrategy:
                  The slice that projects to the first line of the first projection 
                  corresponds to vertical heigth = 0
 
-             In the sample stage reference system:
-                 from vertical height above stage ( pixel units)  ...   {doable_span_v.z_pix_minmax[0]}
-                 up to  (included)                                ...  {doable_span_v.z_pix_minmax[1]}
+             In voxels, the vertical doable span measures: {doable_span_v.z_pix_minmax[1] - doable_span_v.z_pix_minmax[0]}
 
              And in millimiters above the stage:
                  from vertical height above stage ( mm units)  ...   {doable_span_v.z_mm_minmax[0] - self.z_offset_mm }

{nabu-2023.1.0a1.dist-info → nabu-2023.1.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2023.1.0a1
+Version: 2023.1.0a2
 Summary: Nabu - Tomography software
 Author: Pierre Paleo
 Author-email: pierre.paleo@esrf.fr

{nabu-2023.1.0a1.dist-info → nabu-2023.1.0a2.dist-info}/RECORD

@@ -1,11 +1,11 @@
-nabu/__init__.py,sha256=wUgOEqe3zzoUbwRy_FoV5h5hV6zUx9nD3Mniibe1zz0,242
+nabu/__init__.py,sha256=k6HChLxiTiiWaNSvV3_-R7lUf36ntgZfWbjjQg4WVj4,242
 nabu/tests.py,sha256=hzdcjA8MvW_Uxtc5onQ1IpwQotdVPt1KJNEH25uh9JY,1400
 nabu/testutils.py,sha256=nOzearGltWG2fPcJt4JyI_Y4_wzGt2dg_ssaLrH9bHA,10857
 nabu/utils.py,sha256=3o3Xk40xG1ghI6oAuNHJBCXjWcqxAacYijnAD52VDMg,21956
 nabu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/app/bootstrap.py,sha256=kufLeIHgFuDH8S5I9nEodwujNWm7hoTMmPYngXqsXts,3233
 nabu/app/bootstrap_stitching.py,sha256=VxXrgwP7E_k1BhBQ94bEdnxWTQFs-cE5LewlHFr4JI8,733
-nabu/app/cast_volume.py,sha256=NU_bToU3eHwFlMkA_ziY-1cmj3V2ZZyoumwNsvIQTMU,8701
+nabu/app/cast_volume.py,sha256=kreoo5VIOIYoXRHl5cDBO6t_gBL3PP86nAP1Md0xUkU,8921
 nabu/app/cli_configs.py,sha256=BRMW8G7SCLKR_hVy1gxYuBwJy_xdEhMvQ3wh9kzRQB0,14128
 nabu/app/compare_volumes.py,sha256=z9GpnFgcS260Ti8o-DgyUtQgPFrO2CNGhY5aHT7dze8,3327
 nabu/app/composite_cor.py,sha256=MRQqlPziX_ICp5d19OK_6dEJlk8EjZZ-sX7V5tNh_sM,3369
@@ -72,7 +72,7 @@ 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=1n6py13yRng2YRnl3bZFRPfIZNcxYKz93ZDGJWXVQuI,14761
+nabu/io/cast_volume.py,sha256=J0UcvfPlR47wdn_uvzhWYivmhSyS2DOGZo98-nsy91U,15085
 nabu/io/detector_distortion.py,sha256=Or4icugi0fGRKWIG0I9hCuR1UZA5Cel25ZGY7cR2j4I,11744
 nabu/io/reader.py,sha256=nff5uva6HT254HodUNIvIkZECf-F1Kn__ApIqp3kRmM,22555
 nabu/io/reader_helical.py,sha256=_6vZBH-US_VT7oOGJUtYXqPwFws7xZKcmdOthpwvlIQ,4477
@@ -115,7 +115,7 @@ nabu/opencl/utils.py,sha256=vg2QFEA1AMZ2Ky9-iHbk-hKwfDJXGTI0b7Y6h6qYI58,5168
 nabu/pipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/config.py,sha256=aA_DashVEHIaVMCmD2efrezSO6RHw6DO4ZYczKHZr-g,9301
 nabu/pipeline/config_validators.py,sha256=R4QZQq80krovJi_18zS1tD3Am5XDBzwiPujZafPcbko,14025
-nabu/pipeline/datadump.py,sha256=Okrhk5fSLeQZWgo2QBbBwitMcr68blyEBtoj7449zCY,6517
+nabu/pipeline/datadump.py,sha256=Ua4tbzxfGMOiT2-7WZn3IDiJqzzK-TyFuku_XUkH8_Q,6520
 nabu/pipeline/dataset_validator.py,sha256=qsDUfbgYBvXpTbW07LWZ0lMvMut_k9ckiA0Nt1dZN2o,9207
 nabu/pipeline/detector_distortion_provider.py,sha256=ru1AxbcuO-FA8FYooPBWgp1lzdSDUtzFUC1A_sS8jME,920
 nabu/pipeline/estimators.py,sha256=mgjXPTMKHDe4DwwNwAwGqiXUGojzxo_b2FxWWi9bYZQ,32033
@@ -125,7 +125,7 @@ nabu/pipeline/processconfig.py,sha256=iPZRjd3Y1ZTgOUKgYY9F_FKJsEWf4NGGcsy_3JtR7w
 nabu/pipeline/utils.py,sha256=5I0dmJqfIXki2DNFUvcf2enQWb3--vz4RzwHv1rnl18,2730
 nabu/pipeline/writer.py,sha256=IS_1PMQubVq-ra_CydJT4dnVqD7xf3Ak-faP-nASTMs,10920
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/fullfield/chunked.py,sha256=oRncu0ONIch4Aq49W6fvFn3m12S9qRn4dH17H_-KLPQ,35751
+nabu/pipeline/fullfield/chunked.py,sha256=Hjx-57-hCkworNIePFg4RXlpft17wH1eIUwNflFVLfA,36047
 nabu/pipeline/fullfield/chunked_black.py,sha256=HtzVRpcQIAocHpEiPEm7mEYTI6o_XbGezN10jRMCHAw,35285
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=R_X47iZPGNwv6QfvAUAZOrgMc91rpI6NZpcDd3xsDd8,5405
 nabu/pipeline/fullfield/chunked_fb.py,sha256=ikuXkqXc72ES3dB5E96TsfEgn1-lWfd2WaBMYazxifk,36425
@@ -146,11 +146,11 @@ nabu/pipeline/helical/filtering.py,sha256=A5X1_Iwc5Z2X15UfSkejCoDUnmgzrCeWAlqLeK
 nabu/pipeline/helical/gridded_accumulator.py,sha256=hwwC00A-mIZKBqYtr9HatgOaFGDj4Ljzy4FIehe_k1U,20672
 nabu/pipeline/helical/helical_chunked_regridded.py,sha256=E_catWoX_ZCnv0_fN_RBA4FBKQwb9pBR74ChQPVJalw,62389
 nabu/pipeline/helical/helical_chunked_regridded_cuda.py,sha256=tl5qIzYmqWOauFmW46WQoHdU9t9mGDr45m-uOIrYzRk,4013
-nabu/pipeline/helical/helical_reconstruction.py,sha256=GRwEU93gsVir_BfFZXIAbxavB5E9v8_y7xF0U-W7Kok,22341
+nabu/pipeline/helical/helical_reconstruction.py,sha256=hIkwIz9dO8x1VtVDDl0Himz8zsFqcJEDWsCb2hzLx4s,22216
 nabu/pipeline/helical/helical_utils.py,sha256=uFAQHDqENHqQWUpu1n99dnBCCKOlkgjDjvYORY6XFY0,1439
-nabu/pipeline/helical/nabu_config.py,sha256=eX2BvDAT_7q97iWw07B3KTze8udRlzBuux5PgXaKdv0,7296
+nabu/pipeline/helical/nabu_config.py,sha256=DOc16F_r9o4px2wAdRjTRFkBh2K2i8_hHH9-arF8W-g,7299
 nabu/pipeline/helical/processconfig.py,sha256=NMo97gb_uv35EDvfMAi1Emhau8Vua-8eyAzrdk0Ub3E,2571
-nabu/pipeline/helical/span_strategy.py,sha256=dUOThFELV6oyqP15UH82O0M56Hk0hpJj2AQPyeE5D-I,24851
+nabu/pipeline/helical/span_strategy.py,sha256=-IJ8Udqbw2ddmCz0ngAYznVYfLHNoLjxL1ihysbxmsQ,25043
 nabu/pipeline/helical/utils.py,sha256=51Qbh8db6-DX0iB9B9Kb07uwIG6_upAJg_8nhyzbB7o,1555
 nabu/pipeline/helical/weight_balancer.py,sha256=j0TGe50tbbsilQvml9CgMxeSy83CNaifHj-xuMGl8uE,3981
 nabu/pipeline/helical/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -231,10 +231,10 @@ nabu/thirdparty/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtCl6G2NebJlbg,4500
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2023.1.0a1.dist-info/LICENSE,sha256=5Brn2Fb7bFq1aWEGt9Nft51PqVDT8xQmVtQ1kin9nTo,1061
-nabu-2023.1.0a1.dist-info/METADATA,sha256=nW7KllxUbtR-m3xEs7DAT_MBCH4t8iI2Vnnf755MV5s,951
-nabu-2023.1.0a1.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-nabu-2023.1.0a1.dist-info/entry_points.txt,sha256=BEl17rpRKrE3v964P_CCe_Xnd-JgBVBWEp1xySNwm5A,965
-nabu-2023.1.0a1.dist-info/top_level.txt,sha256=4gZBSqkJpZfhO0TPuvtIFnODQGk4j0XQlOsHM9idIv8,5
-nabu-2023.1.0a1.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-nabu-2023.1.0a1.dist-info/RECORD,,
+nabu-2023.1.0a2.dist-info/LICENSE,sha256=5Brn2Fb7bFq1aWEGt9Nft51PqVDT8xQmVtQ1kin9nTo,1061
+nabu-2023.1.0a2.dist-info/METADATA,sha256=SVsaCDC8I6pBboLOjgGFVuZacyIwnefob4piuqVmfvc,951
+nabu-2023.1.0a2.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+nabu-2023.1.0a2.dist-info/entry_points.txt,sha256=BEl17rpRKrE3v964P_CCe_Xnd-JgBVBWEp1xySNwm5A,965
+nabu-2023.1.0a2.dist-info/top_level.txt,sha256=4gZBSqkJpZfhO0TPuvtIFnODQGk4j0XQlOsHM9idIv8,5
+nabu-2023.1.0a2.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
+nabu-2023.1.0a2.dist-info/RECORD,,