nabu 2024.2.0__py3-none-any.whl → 2024.2.0rc2__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0"
+__version__ = "2024.2.0-rc2"
 __nabu_modules__ = [
     "app",
     "cuda",

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 = 0.1  # Hard-coded ?
+            window_fraction = 0.2  # 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.get("side", None) == "from_file":
+        if cor_exec_kwargs["side"] == "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

@@ -668,10 +668,7 @@ 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
-            ),  # COMPAT.
-            "writer_initialized": getattr(self.process_config, "_writer_initialized", False),
+            "single_output_file_initialized": getattr(self.process_config, "single_output_file_initialized", False),
             "raw_vol_metadata": {"voxelSize": self.dataset_info.pixel_size},  # legacy...
         }
         writer_extra_options.update(extra_options)
@@ -856,8 +853,7 @@ 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  # COMPAT.
-        self.process_config._writer_initialized = True
+        self.process_config.single_output_file_initialized = True
 
     def _write_histogram(self):
         if "histogram" not in self.processing_steps:

nabu/pipeline/writer.py

@@ -1,6 +1,5 @@
 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
@@ -114,7 +113,6 @@ 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,
@@ -145,11 +143,6 @@ 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)
@@ -302,7 +302,7 @@ class EDFDatasetAnalyzer(DatasetAnalyzer):
         return np.deg2rad(self.dataset_scanner.rotation_angle())
 
     def get_reduced_flats(self, **reader_kwargs):
-        if self.raw_flats in [None, {}]:
+        if self.flats in [None, {}]:
             raise FileNotFoundError("No reduced flat ('refHST') found in %s" % self.location)
         # A few notes:
         # (1) In principle we could do the reduction (mean/median) from raw frames (ref_xxxx_yyyy)
@@ -311,15 +311,15 @@ class EDFDatasetAnalyzer(DatasetAnalyzer):
         #  (eg. subsampling, binning, distortion correction...)
         # (3) The following spawns one reader instance per file, which is not elegant,
         #   but in principle there are typically 1-2 reduced flats in a scan
-        readers = {k: EDFStackReader([self.raw_flats[k].file_path()], **reader_kwargs) for k in self.raw_flats.keys()}
-        return {k: readers[k].load_data()[0] for k in self.raw_flats.keys()}
+        readers = {k: EDFStackReader([self.flats[k].file_path()], **reader_kwargs) for k in self.flats.keys()}
+        return {k: readers[k].load_data()[0] for k in self.flats.keys()}
 
     def get_reduced_darks(self, **reader_kwargs):
         # See notes in get_reduced_flats() above
-        if self.raw_darks in [None, {}]:
+        if self.darks in [None, {}]:
             raise FileNotFoundError("No reduced dark ('darkend.edf' or 'dark.edf') found in %s" % self.location)
-        readers = {k: EDFStackReader([self.raw_darks[k].file_path()], **reader_kwargs) for k in self.raw_darks.keys()}
-        return {k: readers[k].load_data()[0] for k in self.raw_darks.keys()}
+        readers = {k: EDFStackReader([self.darks[k].file_path()], **reader_kwargs) for k in self.darks.keys()}
+        return {k: readers[k].load_data()[0] for k in self.darks.keys()}
 
     @property
     def files(self):
@@ -365,10 +365,10 @@ class HDF5DatasetAnalyzer(DatasetAnalyzer):
     def _get_dataset_hdf5_url(self):
         if len(self.projections) > 0:
             frames_to_take = self.projections
-        elif len(self.raw_flats) > 0:
-            frames_to_take = self.raw_flats
-        elif len(self.raw_darks) > 0:
-            frames_to_take = self.raw_darks
+        elif len(self.flats) > 0:
+            frames_to_take = self.flats
+        elif len(self.darks) > 0:
+            frames_to_take = self.darks
         else:
             raise ValueError("No projections, no flats and no darks ?!")
         first_proj_idx = sorted(frames_to_take.keys())[0]

{nabu-2024.2.0.dist-info → nabu-2024.2.0rc2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0
+Version: 2024.2.0rc2
 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 <2,>1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py >=3.0
 Requires-Dist: silx >=0.15.0
-Requires-Dist: tomoscan >=2.1.0
+Requires-Dist: tomoscan >=2.1.0a14
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2024.2.0.dist-info → nabu-2024.2.0rc2.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=BeM4pgh4eRU9T-E4ydnqad2Eo39KlEKYGhhvBOzjjGM,270
+nabu/__init__.py,sha256=GU7YEox3KaUtQMTS4mUVSVO6IWhXqQ_Ad6wWGkVsDyk,274
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -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=HcE0xw0ECSkx_kG30taw964rWZwh6lfgg8m9wnKdXik,50415
+nabu/estimation/cor.py,sha256=b8dv047g8AYL9mV6vAAkIloSgNeN3w2bozZY1ox7bII,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
@@ -131,14 +131,14 @@ 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=a-6ISR6ii8J7xMvr6oKFJO8yMFT_QzO7L5kMcg4RJmw,40269
 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=MG_R1oU8Ff9NdKRHiBkLMz0CmvEXY47zBUE-DpjXElQ,8172
+nabu/pipeline/writer.py,sha256=V4b6tGHMj5KpTl2RmDltSP-a-BEw5lfR96cBAdm_6FQ,7649
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/fullfield/chunked.py,sha256=_LauzrZSMO0y6E1g_zYFweK8wb07u1p2JulrVDRnA04,40549
+nabu/pipeline/fullfield/chunked.py,sha256=LxT9LxViYIihgy0N34BgY9uvMlupfJYiX9l6Hp2EdlA,40348
 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
@@ -250,7 +250,7 @@ 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=e3AqYR9ORW9Q03mGYCiC66nXld-X0LPnx9E8X3zFIGU,18568
+nabu/resources/dataset_analyzer.py,sha256=_M7EQcRgldhtGeXCsOUNdx6M1nlLRWW8rKPWMB-lfN0,18518
 nabu/resources/gpu.py,sha256=GgpMb5umRQAUsEDEAefb4wSA5qm4JSMhkWmCEpW3X9g,5702
 nabu/resources/logger.py,sha256=-lOzhN_sU4R3BIfC69aMj2O8S_ocsvXsmwkhWlcxVEc,3758
 nabu/resources/nxflatfield.py,sha256=XlhLYj1TmSQ4s36W48kn0lNTvqXlFCuZxKHfTveltow,9225
@@ -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-2024.2.0.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.0.dist-info/METADATA,sha256=u-pY_1lM9XNtC-flH62tD52Vi6ZTMQFFZjICdc9YoyI,5538
-nabu-2024.2.0.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.2.0.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.0.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.0.dist-info/RECORD,,
+nabu-2024.2.0rc2.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.0rc2.dist-info/METADATA,sha256=nJCwt8-vLEu5ZeqjsatPynMDbqdIILum0iPK23dEqD0,5544
+nabu-2024.2.0rc2.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+nabu-2024.2.0rc2.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.0rc2.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.0rc2.dist-info/RECORD,,