nabu 2024.2.0__tar.gz → 2024.2.0rc2__tar.gz

{nabu-2024.2.0/nabu.egg-info → nabu-2024.2.0rc2}/PKG-INFO

@@ -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>

{nabu-2024.2.0 → nabu-2024.2.0rc2}/nabu/__init__.py

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

{nabu-2024.2.0 → nabu-2024.2.0rc2}/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-2024.2.0 → nabu-2024.2.0rc2}/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-2024.2.0 → nabu-2024.2.0rc2}/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-2024.2.0 → nabu-2024.2.0rc2}/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-2024.2.0 → nabu-2024.2.0rc2}/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 → nabu-2024.2.0rc2/nabu.egg-info}/PKG-INFO

@@ -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>

{nabu-2024.2.0 → nabu-2024.2.0rc2}/nabu.egg-info/requires.txt

@@ -2,7 +2,7 @@ numpy<2,>1.9.0
 scipy
 h5py>=3.0
 silx>=0.15.0
-tomoscan>=2.1.0
+tomoscan>=2.1.0a14
 psutil
 pytest
 tifffile

{nabu-2024.2.0 → nabu-2024.2.0rc2}/pyproject.toml

@@ -53,7 +53,7 @@ dependencies = [
     "scipy",
     "h5py>=3.0",
     "silx >= 0.15.0",
-    "tomoscan >= 2.1.0",
+    "tomoscan >= 2.1.0a14",
     "psutil",
     "pytest",
     "tifffile",