nabu 2024.2.0rc3__py3-none-any.whl → 2024.2.1__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc3"
+__version__ = "2024.2.1"
 __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/estimation/cor.py

@@ -239,7 +239,7 @@ class CenterOfRotationSlidingWindow(CenterOfRotation):
                 win_2_start = img_width // 2 - window_shift
         else:
             abs_pos = int(side + img_width // 2)
-            window_fraction = 0.2  # Hard-coded ?
+            window_fraction = 0.1  # Hard-coded ?
 
             window_width = round(window_fraction * img_width)
             window_shift = window_width // 2

nabu/pipeline/estimators.py

@@ -243,13 +243,13 @@ class CORFinder(CORFinderBase):
         # All find_shift() methods in self.search_methods have the same API with "img_1" and "img_2"
         cor_exec_kwargs = update_func_kwargs(self.cor_finder.find_shift, self.cor_options)
         cor_exec_kwargs["return_relative_to_middle"] = False
-        # FIXME
+        # ----- FIXME -----
         # 'self.cor_options' can contain 'side="from_file"', and we should not modify it directly
         # because it's entered by the user.
         # Either make a copy of self.cor_options, or change the inspect() mechanism
-        if cor_exec_kwargs["side"] == "from_file":
+        if cor_exec_kwargs.get("side", None) == "from_file":
             cor_exec_kwargs["side"] = self._lookup_side or "center"
-        #
+        # ------
         if self._lookup_side is not None:
             cor_exec_kwargs["side"] = self._lookup_side
         self.logger.debug("%s.find_shift(%s)" % (self.cor_finder.__class__.__name__, str(cor_exec_kwargs)))

nabu/pipeline/fullfield/chunked.py

@@ -668,7 +668,10 @@ class ChunkedPipeline:
             "jpeg2000_compression_ratio": options["jpeg2000_compression_ratio"],
             "float_clip_values": options["float_clip_values"],
             "tiff_single_file": options.get("tiff_single_file", False),
-            "single_output_file_initialized": getattr(self.process_config, "single_output_file_initialized", False),
+            "single_output_file_initialized": getattr(
+                self.process_config, "single_output_file_initialized", False
+            ),  # COMPAT.
+            "writer_initialized": getattr(self.process_config, "_writer_initialized", False),
             "raw_vol_metadata": {"voxelSize": self.dataset_info.pixel_size},  # legacy...
         }
         writer_extra_options.update(extra_options)
@@ -853,7 +856,8 @@ class ChunkedPipeline:
         self.writer.write_data(data)
         self.logger.info("Wrote %s" % self.writer.fname)
         self._write_histogram()
-        self.process_config.single_output_file_initialized = True
+        self.process_config.single_output_file_initialized = True  # COMPAT.
+        self.process_config._writer_initialized = True
 
     def _write_histogram(self):
         if "histogram" not in self.processing_steps:

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/pipeline/writer.py

@@ -1,5 +1,6 @@
 from os import path
 from tomoscan.esrf import TIFFVolume, MultiTIFFVolume, EDFVolume, JP2KVolume
+from tomoscan.esrf.volume.singleframebase import VolumeSingleFrameBase
 from ..utils import check_supported, get_num_threads
 from ..resources.logger import LoggerOrPrint
 from ..io.writer import NXProcessWriter, HSTVolVolume, NXVolVolume
@@ -113,6 +114,7 @@ class WriterManager:
         return vol_writer.data_url.file_path()
 
     def _init_writer(self):
+        self._writer_was_already_initialized = self.extra_options.get("writer_initialized", False)
         if self.file_format in ["tiff", "edf", "jp2", "hdf5"]:
             writer_kwargs = {
                 "folder": self.output_dir,
@@ -143,6 +145,11 @@ class WriterManager:
         self._h5_entry = self.metadata.get("entry", "entry")
         self.writer = self._writer_classes[self.file_format](**writer_kwargs)
         self.fname = self.get_fname(self.writer)
+        # In certain cases, tomoscan needs to remove any previous existing volume filess
+        # and avoid calling 'clean_output_data' when writing downstream (for chunk processing)
+        if isinstance(self.writer, VolumeSingleFrameBase):
+            self.writer.skip_existing_data_files_removal = self._writer_was_already_initialized
+        # ---
         if path.exists(self.fname):
             err = "File already exists: %s" % self.fname
             if self.overwrite:

nabu/resources/dataset_analyzer.py

@@ -52,7 +52,7 @@ class DatasetAnalyzer:
             "output_dir": None,
             "exclude_projections": None,
             "hdf5_entry": None,
-            "nx_version": 1.0,
+            # "nx_version": 1.0,
         }
         # --
         advanced_options.update(extra_options)

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-2024.2.0rc3.dist-info → nabu-2024.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc3
+Version: 2024.2.1
 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-2024.2.0rc3.dist-info → nabu-2024.2.1.dist-info}/RECORD

@@ -1,7 +1,7 @@
 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=nj3TOWBu8oPUoBNHU2H_cND8gzxtol3hSVTR0ewGpTM,274
+nabu/__init__.py,sha256=_crjpH1e06xe5ACe0WGTWJwi-ZGm59UWsB_3tUnYxlA,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -9,7 +9,7 @@ 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
@@ -64,7 +64,7 @@ nabu/cuda/src/transpose.cu,sha256=Enim7vLxTCFZbK3BmYdQ6ZatA_FLp6601VOSl8iGFjg,47
 nabu/cuda/tests/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 nabu/estimation/__init__.py,sha256=HWE3ivArjlJx4FjFh2Q73VmpIyzod80KTmXvFo1AP1s,379
 nabu/estimation/alignment.py,sha256=DWe4PBLsAOt95m_UEinVXUhXyYDmV0NOHW-oHpVEjVk,21185
-nabu/estimation/cor.py,sha256=b8dv047g8AYL9mV6vAAkIloSgNeN3w2bozZY1ox7bII,50415
+nabu/estimation/cor.py,sha256=HcE0xw0ECSkx_kG30taw964rWZwh6lfgg8m9wnKdXik,50415
 nabu/estimation/cor_sino.py,sha256=Wh0t8Ak6h8kf3rn5azD1XqD4e0Xa90oZUy90n9Ory8c,19116
 nabu/estimation/distortion.py,sha256=DEXizQpgHBXmrhbQ0kuEchicxmiDgmU2qrh8bCgSezg,4701
 nabu/estimation/focus.py,sha256=I2B5ODmGToE0-Y-B_6v1zJv7XcWdkXPZzrs2uYpiPlc,18029
@@ -131,20 +131,20 @@ 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=a-6ISR6ii8J7xMvr6oKFJO8yMFT_QzO7L5kMcg4RJmw,40269
+nabu/pipeline/estimators.py,sha256=AZXDmz7hngbVEfytpcu3E2QkOG4IqtXjQN8uUMBJTa0,40298
 nabu/pipeline/params.py,sha256=EoovjCUTUXmj5HQ3qE0RhP7XD3cndaiT21TdvjTIhE8,3746
 nabu/pipeline/processconfig.py,sha256=3xx2Lc8uEzPAqSMwUncr4RCiCtKn2c7wnXXbPSn8GNo,7719
 nabu/pipeline/reader.py,sha256=wkxPHYOi_C8dHNc7kddB8AMtFuW7GjsP_tm6SJeHlEY,4792
 nabu/pipeline/utils.py,sha256=0O1GLyYLQ8oA2ErI_T3BIfEVjP48dl-u_gl91eX7pjU,3543
-nabu/pipeline/writer.py,sha256=V4b6tGHMj5KpTl2RmDltSP-a-BEw5lfR96cBAdm_6FQ,7649
+nabu/pipeline/writer.py,sha256=MG_R1oU8Ff9NdKRHiBkLMz0CmvEXY47zBUE-DpjXElQ,8172
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/fullfield/chunked.py,sha256=LxT9LxViYIihgy0N34BgY9uvMlupfJYiX9l6Hp2EdlA,40348
+nabu/pipeline/fullfield/chunked.py,sha256=_LauzrZSMO0y6E1g_zYFweK8wb07u1p2JulrVDRnA04,40549
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=Jdkk6ZIt3S6UZYbupHtSj2vrj3krWMcqRHHprfblDfk,5848
 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
@@ -250,10 +250,10 @@ nabu/reconstruction/tests/test_reconstructor.py,sha256=3p2Wk_OqgZqkNOkhK_NJWlHkO
 nabu/reconstruction/tests/test_sino_normalization.py,sha256=fGv5Dlidxgm8ZC70Nk6oqVgpY2jzOW9NJaGlo44IJOo,3692
 nabu/resources/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/resources/cor.py,sha256=-mcrTbj3G7o4PP5E_gIRo2j6_-ADmMkkOc_0CyQv84c,170
-nabu/resources/dataset_analyzer.py,sha256=I79-QEFrWG7Zc6O6134sLfNpj3_VmAei-1Io-zuPCts,18566
+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
@@ -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-2024.2.0rc3.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.0rc3.dist-info/METADATA,sha256=DtswpBFRHCRI-w--UzSZ9Mp1Zc8R-xBjBfcCYRzCJPs,5541
-nabu-2024.2.0rc3.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.2.0rc3.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.0rc3.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.0rc3.dist-info/RECORD,,
+nabu-2024.2.1.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.1.dist-info/METADATA,sha256=XlEefB-apFg-XrbRJ-uOM18VdoqY-MXyiqO77-l3_m4,5538
+nabu-2024.2.1.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+nabu-2024.2.1.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.1.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.1.dist-info/RECORD,,