nabu 2024.1.3__py3-none-any.whl → 2024.1.5__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.3"
+__version__ = "2024.1.5"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/pipeline/dataset_validator.py

@@ -157,8 +157,9 @@ class DatasetValidatorBase:
         """
         dataset_cfg = self.nabu_config["dataset"]
         self.binning = (dataset_cfg["binning"], dataset_cfg["binning_z"])
-        subsampling_factor, subsampling_begin = dataset_cfg["projections_subsampling"]
+        subsampling_factor, subsampling_start = dataset_cfg["projections_subsampling"]
         self.subsampling_factor = subsampling_factor or 1
+        self.subsampling_start = subsampling_start or 0
 
         if self.binning != (1, 1):
             bin_x, bin_z = self.binning

nabu/pipeline/fullfield/processconfig.py

@@ -83,6 +83,10 @@ class ProcessConfig(ProcessConfigBase):
             )
         self.rec_params = self.nabu_config["reconstruction"]
 
+        subsampling_factor, subsampling_start = self.nabu_config["dataset"]["projections_subsampling"]
+        self.subsampling_factor = subsampling_factor or 1
+        self.subsampling_start = subsampling_start or 0
+
         self._update_dataset_with_user_overwrites()
         self._get_rotation_axis_position()
         self._update_rotation_angles()
@@ -118,8 +122,9 @@ class ProcessConfig(ProcessConfigBase):
         if transl_file is not None and "://" not in transl_file:
             try:
                 translations = get_values_from_file(
-                    transl_file, shape=(self.dataset_info.n_angles, last_dim), any_size=True
+                    transl_file, shape=(self.n_angles(subsampling=False), last_dim), any_size=True
                 ).astype(np.float32)
+                translations = translations[self.subsampling_start :: self.subsampling_factor]
             except ValueError:
                 print("Something wrong with translation_movements_file %s" % transl_file)
                 raise
@@ -145,9 +150,10 @@ class ProcessConfig(ProcessConfigBase):
             try:
                 axis_correction = get_values_from_file(
                     axis_correction_file,
-                    n_values=self.dataset_info.n_angles,
+                    n_values=self.n_angles(subsampling=False),
                     any_size=True,
                 ).astype(np.float32)
+                axis_correction = axis_correction[self.subsampling_start :: self.subsampling_factor]
             except ValueError:
                 print("Something wrong with axis correction file %s" % axis_correction_file)
                 raise
@@ -225,7 +231,7 @@ class ProcessConfig(ProcessConfigBase):
         self.logger.debug("Doing coupled validation")
         self._dataset_validator = FullFieldDatasetValidator(self.nabu_config, self.dataset_info)
         # Not so ideal to propagate fields like this
-        for what in ["rec_params", "rec_region", "binning", "subsampling_factor"]:
+        for what in ["rec_params", "rec_region", "binning"]:
             setattr(self, what, getattr(self._dataset_validator, what))
 
     #
@@ -255,7 +261,7 @@ class ProcessConfig(ProcessConfigBase):
     def n_angles(self, subsampling=False):
         rot_angles = self.dataset_info.rotation_angles
         if subsampling:
-            rot_angles = rot_angles[:: (self.subsampling or 1)]
+            rot_angles = rot_angles[self.subsampling_start :: self.subsampling_factor]
         return len(rot_angles)
 
     def radios_shape(self, binning=False, subsampling=False):
@@ -300,10 +306,12 @@ class ProcessConfig(ProcessConfigBase):
         return sorted(self.dataset_info.projections.keys())[::step]
 
     def rotation_angles(self, subsampling=False):
+        start = 0
         step = 1
         if subsampling:
-            step = self.subsampling or 1
-        return self.dataset_info.rotation_angles[::step]
+            start = self.subsampling_start
+            step = self.subsampling_factor
+        return self.dataset_info.rotation_angles[start::step]
 
     @property
     def rec_roi(self):
@@ -512,7 +520,7 @@ class ProcessConfig(ProcessConfigBase):
         translations = dataset_info.translations
         if translations is not None:
             tasks.append("radios_movements")
-            options["radios_movements"] = {"translation_movements": dataset_info.translations[:: self.binning_z]}
+            options["radios_movements"] = {"translation_movements": dataset_info.translations}
         #
         # Sinogram normalization (before half-tomo)
         #
@@ -562,7 +570,8 @@ class ProcessConfig(ProcessConfigBase):
             rec_options["enable_halftomo"] = self.do_halftomo
             rec_options["axis_correction"] = dataset_info.axis_correction
             if dataset_info.axis_correction is not None:
-                rec_options["axis_correction"] = rec_options["axis_correction"][:: self.subsampling_factor]
+                rec_options["axis_correction"] = rec_options["axis_correction"]
+
             rec_options["angles"] = np.array(self.rotation_angles(subsampling=True))
             rec_options["angles"] += np.deg2rad(nabu_config["reconstruction"]["angle_offset"])
             voxel_size = dataset_info.pixel_size * 1e-4

nabu/pipeline/tests/test_chunk_reader.py

@@ -55,10 +55,6 @@ class TestChunkReader:
         first_sino_odd = reader.data[:, 0, :].copy()
         compacted_dataslices_odd = get_compacted_dataslices_as_sorted_tuples(reader)
 
-        # from spire.utils import ims
-        # ims([first_sino_all[::2], first_sino_even, first_sino_all[::2]*1. - first_sino_even])
-        # ims([first_sino_all[::2], first_sino_even, first_sino_all[1::2]*1. - first_sino_odd])
-
         # Check that the compacted data slices are correct
         assert len(compacted_dataslices_all) == len(compacted_dataslices_even) == len(compacted_dataslices_odd)
         for data_slice_all, data_slice_even, data_slice_odd in zip(

nabu/pipeline/writer.py

@@ -136,8 +136,9 @@ class WriterManager:
                 ),
                 "overwrite": self.overwrite,
                 "append": self.extra_options.get("single_output_file_initialized", False),
-                "hst_metadata": self.extra_options.get("raw_vol_metadata", {}),
             }
+            if self.file_format == "vol":
+                writer_kwargs["hst_metadata"] = self.extra_options.get("raw_vol_metadata", {})
         else:
             raise ValueError("Unsupported file format: %s" % self.file_format)
         self._h5_entry = self.metadata.get("entry", "entry")

nabu/utils.py

@@ -422,19 +422,6 @@ def copy_dict_items(dict_, keys):
     return res
 
 
-def remove_first_dict_items(dict_, n_items, sort_func=None, inplace=True):
-    """
-    Remove the first items of a dictionary. The keys have to be sortable
-    """
-    sorted_keys = sorted(dict_.keys(), key=sort_func)
-    if inplace:
-        for key in sorted_keys[:n_items]:
-            dict_.pop(key)
-        return dict_
-    else:
-        return copy_dict_items(dict_, sorted_keys[n_items:])
-
-
 def recursive_copy_dict(dict_):
     """
     Perform a shallow copy of a dictionary of dictionaries.

{nabu-2024.1.3.dist-info → nabu-2024.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.3
+Version: 2024.1.5
 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-2024.1.3.dist-info → nabu-2024.1.5.dist-info}/RECORD

@@ -2,10 +2,10 @@ doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
 doc/doc_config.py,sha256=anqeOVjqE2e7eVzg7yuh9dvIneTkrA5doGl1cVBqT7Q,730
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=0gCFkw19XEtpFmj4__mgFLwZHUBVLIJtgG-XzgYhmMQ,270
+nabu/__init__.py,sha256=ErLZd1sdO03iHW__3mBKndACl9sfSWOQdVChBK2wp70,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=qqtGgkIhpOpXhgeoXlqCb91Rx-JlI4ALaDF6nt8YRRk,13298
-nabu/utils.py,sha256=1OKKhQ6-t7OOwTLQkTJuK5Hk9lb7hkEZrDtTdcmvD4c,24164
+nabu/utils.py,sha256=w-xfRb6TFQpS-tao6nlvfmr962pmeec-WH1GltSUCrk,23767
 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
@@ -127,21 +127,21 @@ nabu/pipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/config.py,sha256=amc05PX0kZA5wHjD1oFP59MfW4pBA-gjBypy4tKLnv0,9221
 nabu/pipeline/config_validators.py,sha256=rvK1Q_KmA1LUeNTefNxXCpYfDQ1zAdk1kFePrLintwc,16300
 nabu/pipeline/datadump.py,sha256=Ua4tbzxfGMOiT2-7WZn3IDiJqzzK-TyFuku_XUkH8_Q,6520
-nabu/pipeline/dataset_validator.py,sha256=b6RYIoaElX8QkqYPFl7KsMU7wai7jJjG6QtTQBvPd_o,9207
+nabu/pipeline/dataset_validator.py,sha256=etQw9NC_YGsdWCgjsn8aJ3WfvcRuJlLVZlWoqhvvo-8,9263
 nabu/pipeline/detector_distortion_provider.py,sha256=ru1AxbcuO-FA8FYooPBWgp1lzdSDUtzFUC1A_sS8jME,920
 nabu/pipeline/estimators.py,sha256=4V5pwl5vUFMJDanWnmw7POnSsa9lKyKtUzvq9GLcJwc,41374
 nabu/pipeline/fallback_utils.py,sha256=7ccrKYE-rp3fydb72VA6W0_eKcEoqYBEAPlmij_lyEc,6086
 nabu/pipeline/params.py,sha256=VdrekcxOnbrMzvvLcwEWINiMM0uVKmPxJJBwp3lhHBg,3479
 nabu/pipeline/processconfig.py,sha256=3wCobeC_gI9OTO7v0Hk-IeEJUdKoavK-OzKLd1da5Dg,8216
 nabu/pipeline/utils.py,sha256=NONAgBfTfUYvBNfoTqD33MAYaPZyCJL10SnR6B0lLec,3462
-nabu/pipeline/writer.py,sha256=mUpD0kNHrPQhnHwybMMxA7pjaKi53aP8QLBJsqEcQ-4,7501
+nabu/pipeline/writer.py,sha256=0ts40VNN3RiRURvZ2gNqsigsAJuwcjnYF4RJ15qaMpI,7558
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/fullfield/chunked.py,sha256=qGE9gpww2zPbtPeM1Fe0RPRhl3onqxs8fr3HRug-x6I,36919
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=aGzjY8MX6OL8auEj6Y0RfOGCmFnczsdfj6-8Net5AbQ,5645
 nabu/pipeline/fullfield/computations.py,sha256=VpIURVXh8EpNSfait_AIFM4Ci-GK_546Wkb-Wn9r31Y,9935
 nabu/pipeline/fullfield/dataset_validator.py,sha256=sRgUECUc8aOjFbwrW-dHjvIf7K3T40YPSIgt3cInKAc,3055
 nabu/pipeline/fullfield/nabu_config.py,sha256=a0mMoLkvlvHgX6RmUS1m1UhJS-XB3O6wBCnkNoI90Cs,30358
-nabu/pipeline/fullfield/processconfig.py,sha256=SzA9FA7aK5V13q8f8fFmKvumvK0ATkl5Bi_lAs2r8m8,35658
+nabu/pipeline/fullfield/processconfig.py,sha256=ad2lmo-cCkzfDJqMd__FhbfIInndTxQsLdgH9Ec9Tzc,36107
 nabu/pipeline/fullfield/reconstruction.py,sha256=Km_ZDtoiDQdX3TdTh6E9bzS5hoMC0jYU5eZWodaLbIg,36627
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/helical/dataset_validator.py,sha256=0YQc0hdYdpaXznFaKmlj9SIu7mNs0xXMejcRkhOZHaI,640
@@ -161,7 +161,7 @@ nabu/pipeline/helical/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 nabu/pipeline/helical/tests/test_accumulator.py,sha256=nNHwqUgSyUpdZVYNVyxqekj0SoThCF8s-8o3NfSw6vI,6416
 nabu/pipeline/helical/tests/test_pipeline_elements_full.py,sha256=zeR9SaeD0mnhtKU7qo4Qrn_lg1I1Vhg4dqzj6jy8tpg,14569
 nabu/pipeline/helical/tests/test_strategy.py,sha256=rt8SsUHBMMcVFl48kRGcOyf1y4bYqaA2xDznQxE7wFs,2721
-nabu/pipeline/tests/test_chunk_reader.py,sha256=Z5N620l4jZmG_15v5GPbqf4LgZeO2hJvcsptq_YpltU,3641
+nabu/pipeline/tests/test_chunk_reader.py,sha256=OB279hSvgmVhWv_OauZNWTJeaaiheETayGYK79Op10Q,3410
 nabu/pipeline/tests/test_estimators.py,sha256=6VK7fxxfrRTWSSi2bhHqbLy8pZJ2DALO1gJkuxpLDSQ,8392
 nabu/pipeline/xrdct/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/preproc/__init__.py,sha256=dKxvZvWZXjKS3iPRaSXiUeM2dNGIOyTlirq5pdAWY0Y,284
@@ -288,9 +288,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 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-2024.1.3.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.1.3.dist-info/METADATA,sha256=9F-UcdLnNHr8HNiwZOdq_TeA2eowj38U4hVcKCWpcEM,5224
-nabu-2024.1.3.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-nabu-2024.1.3.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.1.3.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.1.3.dist-info/RECORD,,
+nabu-2024.1.5.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.1.5.dist-info/METADATA,sha256=HAJhXAjP2N1CTDrVr05k1DoPF75hrfRtbTG2c5qccdw,5224
+nabu-2024.1.5.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+nabu-2024.1.5.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.1.5.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.1.5.dist-info/RECORD,,