nabu 2024.2.0rc4__py3-none-any.whl → 2024.2.2__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc4"
+__version__ = "2024.2.2"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/app/cli_configs.py

@@ -37,7 +37,7 @@ BootstrapConfig = {
         "default": "",
     },
     "template": {
-        "help": "Use a template configuration file. Available are: id19_pag, id16_holo, id16_ctf. You can also define your own templates via the NABU_TEMPLATES_PATH environment variable.",
+        "help": "Use a template configuration file. Available are: id19_pag, id16_holo, id16_ctf, id16a_fluo, bm05_pag. You can also define your own templates via the NABU_TEMPLATES_PATH environment variable.",
         "default": "",
     },
     "helical": {"help": "Prepare configuration file for helical", "default": 0, "required": False, "type": int},

nabu/pipeline/estimators.py

@@ -89,11 +89,13 @@ def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logg
         estimated_cor = cor_finder.find_cor()
     else:
         composite_options = update_func_kwargs(CompositeCORFinder, cor_options)
-        for what in ["cor_options", "logger"]:
+        for what in ["cor_options", "logger", "do_flatfield"]:
             composite_options.pop(what, None)
         cor_finder = CompositeCORFinder(
             dataset_info,
             cor_options=cor_options,
+            do_flatfield=do_flatfield,
+            take_log=cor_options.get("take_log", True),
             logger=logger,
             **composite_options,
         )
@@ -451,6 +453,7 @@ class CompositeCORFinder(CORFinderBase):
         oversampling=4,
         theta_interval=5,
         n_subsampling_y=40,
+        do_flatfield=True,
         take_log=True,
         cor_options=None,
         spike_threshold=0.04,
@@ -458,7 +461,7 @@ class CompositeCORFinder(CORFinderBase):
         norm_order=1,
     ):
         super().__init__(
-            "composite-coarse-to-fine", dataset_info, do_flatfield=True, cor_options=cor_options, logger=logger
+            "composite-coarse-to-fine", dataset_info, do_flatfield=False, cor_options=cor_options, logger=logger
         )
         if norm_order not in [1, 2]:
             raise ValueError(
@@ -535,7 +538,10 @@ class CompositeCORFinder(CORFinderBase):
 
         self.absolute_indices = sorted(self.dataset_info.projections.keys())
 
-        my_flats = self.dataset_info.flats
+        if do_flatfield:
+            my_flats = self.dataset_info.flats
+        else:
+            my_flats = None
 
         if my_flats is not None and len(list(my_flats.keys())):
             self.use_flat = True

nabu/pipeline/fullfield/processconfig.py

@@ -465,7 +465,7 @@ class ProcessConfig(ProcessConfigBase):
         if self.get_radios_rotation_mode() == "chunk":
             tasks.append("tilt_correction")
             options["tilt_correction"] = {
-                "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
+                "angle": dataset_info.detector_tilt,
                 "center": nabu_config["preproc"]["rotate_projections_center"],
                 "mode": "chunk",
             }
@@ -513,7 +513,7 @@ class ProcessConfig(ProcessConfigBase):
         if self.get_radios_rotation_mode() == "full":
             tasks.append("tilt_correction")
             options["tilt_correction"] = {
-                "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
+                "angle": dataset_info.detector_tilt,
                 "center": nabu_config["preproc"]["rotate_projections_center"],
                 "mode": "full",
             }

nabu/pipeline/fullfield/reconstruction.py

@@ -253,7 +253,7 @@ class FullFieldReconstructor:
         if self.process_config.processing_options.get("phase", {}).get("method", None) == "CTF":
             force_grouped_mode = True
             msg = "CTF phase retrieval needs to process full radios"
-        if self.process_config.processing_options.get("tilt_correction", {}).get("angle", 0) > 15:
+        if (self.process_config.dataset_info.detector_tilt or 0) > 15:
             force_grouped_mode = True
             msg = "Radios rotation with a large angle needs to process full radios"
         if self.process_config.resume_from_step == "sinogram" and force_grouped_mode:

nabu/resources/nxflatfield.py

@@ -35,12 +35,10 @@ def get_frame_possible_urls(dataset_info, user_dir, output_dir):
         else:
             dataurl_default_template = h5scan.REDUCED_DARKS_DATAURLS[0]
 
-        rel_file_path = dataurl_default_template.file_path().format(
-            scan_prefix=dataset_info.dataset_scanner.get_dataset_basename()
-        )
+        rel_file_path = dataurl_default_template.file_path().format(scan_prefix=h5scan.get_dataset_basename())
         return DataUrl(
             file_path=os.path.join(dirname, rel_file_path),
-            data_path=dataurl_default_template.data_path(),
+            data_path=dataurl_default_template.data_path().format(entry=h5scan.entry, index="{index}"),
             data_slice=dataurl_default_template.data_slice(),  # not sure if needed
             scheme="silx",
         )
@@ -144,9 +142,11 @@ def data_url_exists(data_url):
     """
     if not (os.path.isfile(data_url.file_path())):
         return False
+    group_exists = False
     with HDF5File(data_url.file_path(), "r") as f:
-        path_exists = f.get(data_url.data_path(), default=None) is not None
-    return path_exists
+        data_path_without_index = data_url.data_path().split("{")[0]
+        group_exists = f.get(data_path_without_index, default=None) is not None
+    return group_exists
 
 
 # pylint: disable=E1136

nabu/stitching/config.py

@@ -1038,8 +1038,9 @@ class PreProcessedSingleAxisStitchingConfiguration(SingleAxisStitchingConfigurat
                 config[STITCHING_SECTION].get(ALIGNMENT_AXIS_2_FIELD, AlignmentAxis2.CENTER)
             ),
             pad_mode=config[STITCHING_SECTION].get(PAD_MODE_FIELD, "constant"),
-            duplicate_data=not config[STITCHING_SECTION].get(AVOID_DATA_DUPLICATION_FIELD, False),
-            normalization_by_sample=NormalizationBySample.from_dict(config.get(NORMALIZATION_BY_SAMPLE_SECTION, {})),
+            duplicate_data=not _scalar_or_tuple_to_bool_or_tuple_of_bool(
+                config[STITCHING_SECTION].get(AVOID_DATA_DUPLICATION_FIELD, False)
+            ),
         )
 
 
@@ -1196,7 +1197,9 @@ class PostProcessedSingleAxisStitchingConfiguration(SingleAxisStitchingConfigura
                 config[STITCHING_SECTION].get(ALIGNMENT_AXIS_2_FIELD, AlignmentAxis2.CENTER)
             ),
             pad_mode=config[STITCHING_SECTION].get(PAD_MODE_FIELD, "constant"),
-            duplicate_data=not config[STITCHING_SECTION].get(AVOID_DATA_DUPLICATION_FIELD, False),
+            duplicate_data=not _scalar_or_tuple_to_bool_or_tuple_of_bool(
+                config[STITCHING_SECTION].get(AVOID_DATA_DUPLICATION_FIELD, False)
+            ),
             normalization_by_sample=NormalizationBySample.from_dict(config.get(NORMALIZATION_BY_SAMPLE_SECTION, {})),
         )
 

{nabu-2024.2.0rc4.dist-info → nabu-2024.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc4
+Version: 2024.2.2
 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-2024.2.0rc4.dist-info → nabu-2024.2.2.dist-info}/RECORD

@@ -2,7 +2,7 @@ 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=NEQPS4U8T5nfg0_kumGk9YWMlO5RkFqOihedIBF9z_A,274
+nabu/__init__.py,sha256=c4AaFlxaEks7K6XWAPy5va8o7QnA79fGW45T36l46to,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -10,7 +10,7 @@ nabu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/app/bootstrap.py,sha256=3yLZJmrmQBmPJMBtE2ih2cspfqOy5T_UN2U8B3i_hkI,3266
 nabu/app/bootstrap_stitching.py,sha256=Inr0_zRAtyeMTK1BKxGqoDf-Na0O33CICmQJYja06ug,2148
 nabu/app/cast_volume.py,sha256=mjINEIFrh2BVC8mPFO0cnzlFUOS3x5aqjFPGKsb3H-c,11264
-nabu/app/cli_configs.py,sha256=frcKu4Pp6380Gf2j0loP8OYqVRlTcjlLQBHe1mGJR_A,22254
+nabu/app/cli_configs.py,sha256=EGKp7DrR48PAahZLJd09XAIAdm7Q5nOVSybztglhW_8,22276
 nabu/app/compare_volumes.py,sha256=Mu5O4uP-ANo-el-fE5PLvEq42BTk5FkrscaFRyQZdis,3341
 nabu/app/composite_cor.py,sha256=TjYiAtmY4o9lwNpkIEueTTNli72QN6jtR_zbtCeOJz4,5138
 nabu/app/correct_rot.py,sha256=K0UQz4l5caFvsSr1-1y5hZvt6e45NAH3qYOhzHm2mGc,2130
@@ -131,7 +131,7 @@ nabu/pipeline/config_validators.py,sha256=ocAKB26iRjm5qs1Ay4B_rgGcg8aZjAP34XpEZR
 nabu/pipeline/datadump.py,sha256=lK36YlsVSeE4fdkD7cgVCl4RKn-Wa9KYgOw4DNtH8Ow,6982
 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=AZXDmz7hngbVEfytpcu3E2QkOG4IqtXjQN8uUMBJTa0,40298
+nabu/pipeline/estimators.py,sha256=AF7Nzbj9vPHfW5_ivo3_64D1Ct4RYqeOHx6tb1Phf30,40508
 nabu/pipeline/params.py,sha256=EoovjCUTUXmj5HQ3qE0RhP7XD3cndaiT21TdvjTIhE8,3746
 nabu/pipeline/processconfig.py,sha256=3xx2Lc8uEzPAqSMwUncr4RCiCtKn2c7wnXXbPSn8GNo,7719
 nabu/pipeline/reader.py,sha256=wkxPHYOi_C8dHNc7kddB8AMtFuW7GjsP_tm6SJeHlEY,4792
@@ -143,8 +143,8 @@ nabu/pipeline/fullfield/chunked_cuda.py,sha256=Jdkk6ZIt3S6UZYbupHtSj2vrj3krWMcqR
 nabu/pipeline/fullfield/computations.py,sha256=AEp3qvwyY-l8-GzjH1E6kmcmU6OgDp6sB-mltq0Jnxg,9970
 nabu/pipeline/fullfield/dataset_validator.py,sha256=Iy6oOnXnBldDcg0ifm_zzrzMQ6YdkR_hkHFySZgxbno,2943
 nabu/pipeline/fullfield/nabu_config.py,sha256=rvHmCNHx2y-GKBidRWCAjJd0IynvolPTTmBqNoOSvEA,31877
-nabu/pipeline/fullfield/processconfig.py,sha256=SXEWU27xRYfTUyyczuJmn-0IA3A5EsvFpzK0Q47-3HE,36905
-nabu/pipeline/fullfield/reconstruction.py,sha256=nmJWXna6XODOu0GuufSnz3s6fLCZhZrkBUFHII8nudo,37450
+nabu/pipeline/fullfield/processconfig.py,sha256=2eE9W0KjsHq8aSCXlczsISpWM9SMjWL03fN1RqZWyxg,36815
+nabu/pipeline/fullfield/reconstruction.py,sha256=fMHKR8LnpQ2_asIO5bJB3pRixABrKLi53KzJuB83NZ4,37422
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/helical/dataset_validator.py,sha256=0YQc0hdYdpaXznFaKmlj9SIu7mNs0xXMejcRkhOZHaI,640
 nabu/pipeline/helical/fbp.py,sha256=0fAz-Fb0Rn_FzellvcS2cy-Wvm-5dxEf494YFt4pLws,5845
@@ -254,7 +254,7 @@ nabu/resources/cor.py,sha256=-mcrTbj3G7o4PP5E_gIRo2j6_-ADmMkkOc_0CyQv84c,170
 nabu/resources/dataset_analyzer.py,sha256=e3AqYR9ORW9Q03mGYCiC66nXld-X0LPnx9E8X3zFIGU,18568
 nabu/resources/gpu.py,sha256=GgpMb5umRQAUsEDEAefb4wSA5qm4JSMhkWmCEpW3X9g,5702
 nabu/resources/logger.py,sha256=-lOzhN_sU4R3BIfC69aMj2O8S_ocsvXsmwkhWlcxVEc,3758
-nabu/resources/nxflatfield.py,sha256=XlhLYj1TmSQ4s36W48kn0lNTvqXlFCuZxKHfTveltow,9225
+nabu/resources/nxflatfield.py,sha256=FhPqiXe6ZKu5eGI6aVfyTgcHhZF9kQUNX0cOxDPD73k,9324
 nabu/resources/utils.py,sha256=LtOWEYneEzz0mDIpUWM23v9ILJ8FM0YFaVG3fFVc7OU,5725
 nabu/resources/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/resources/templates/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -268,7 +268,7 @@ nabu/resources/tests/test_nxflatfield.py,sha256=XRGbYwqJv0NYAVQnAB224TwTZP_W2Bs3
 nabu/resources/tests/test_units.py,sha256=F2jFTck-1UwYET1MwTtX6ntzYUosfwOJkugSencGgz8,2155
 nabu/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/stitching/alignment.py,sha256=2ehpuWDz38AFAoJk3yA0DXf-18Kb329YaCCBBpa7Txc,9078
-nabu/stitching/config.py,sha256=wxidcHaCfp0LxqKKMFqshS_oECslcgBozIenQOQMJPU,52755
+nabu/stitching/config.py,sha256=CP5g3f4sXpUBLAlG7LRg-90Ebon-janurbuORgYGi1c,52783
 nabu/stitching/definitions.py,sha256=JbmYwXKxOTYCr2LDXbHO-uNE2OLOBm4ir9AQ7e-Q3lY,158
 nabu/stitching/frame_composition.py,sha256=7HebOFzSBirJT-MG10T7dzR8Gu0YVwfJb27LDk8lln4,6687
 nabu/stitching/overlap.py,sha256=JkLM8gNyacEY7BE9vyF8M28Rer97-ExK8ZEvOKeFbPw,17200
@@ -311,9 +311,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=Khe4zFf0kRzu65Yxnvq58gt1ljOztqJGdMDhVAiM7lM,24363
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2024.2.0rc4.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.0rc4.dist-info/METADATA,sha256=X82wyEoBnquYyUlKh6UBebcpBLAS9ieXX7EETWAe068,5541
-nabu-2024.2.0rc4.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-nabu-2024.2.0rc4.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.0rc4.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.0rc4.dist-info/RECORD,,
+nabu-2024.2.2.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.2.dist-info/METADATA,sha256=D8BRBoDIZHm9VsFDcx6ADFq_mxv7n7BtdkbdpU3m2u0,5538
+nabu-2024.2.2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+nabu-2024.2.2.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.2.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.2.dist-info/RECORD,,