nabu 2024.2.0__tar.gz → 2024.2.0rc1__tar.gz

{nabu-2024.2.0/nabu.egg-info → nabu-2024.2.0rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0
+Version: 2024.2.0rc1
 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-2024.2.0rc1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0"
+__version__ = "2024.2.0-rc1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.2.0 → nabu-2024.2.0rc1}/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
@@ -1114,6 +1114,11 @@ class CenterOfRotationOctaveAccurate(CenterOfRotation):
         # ---
         self._check_img_pair_sizes(img_1, img_2)
 
+        if side != "center":
+            msg = "This method cannot handle half acquisition"
+            self.logger.fatal(msg)
+            raise ValueError(msg)
+
         img_shape = img_2.shape
         roi_yxhw = self._determine_roi(img_shape, roi_yxhw)
 

{nabu-2024.2.0 → nabu-2024.2.0rc1}/nabu/estimation/cor_sino.py

@@ -91,7 +91,7 @@ class SinoCor:
                     imax = i
             self.cor_abs = self.sx - (imax + window_width + 1.0) / 2.0
             self.cor_rel = self.sx / 2 - (imax + window_width + 1.0) / 2.0
-        elif side == "left":
+        else:
             for i in nr:
                 imout = self.data1[:, i : i + window_width] - self.data2[:, self.sx - window_width : self.sx]
                 diff = imout.max() - imout.min()
@@ -100,8 +100,6 @@ class SinoCor:
                     imax = i
             self.cor_abs = (imax + window_width - 1.0) / 2
             self.cor_rel = self.cor_abs - self.sx / 2.0 - 1
-        else:
-            raise ValueError(f"Invalid side given ({side}). should be 'left' or 'right'")
         if imax < 1:
             self.logger.warning("sliding width %d seems too large!" % window_width)
         self.rcor_abs = round(self.cor_abs)

{nabu-2024.2.0 → nabu-2024.2.0rc1}/nabu/pipeline/estimators.py

@@ -31,21 +31,6 @@ from .params import cor_methods, tilt_methods
 
 
 def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logger=None):
-    """
-    High level function to compute the center of rotation (COR)
-
-    Parameters
-    ----------
-    method: name of the method to be used for computing the center of rotation
-    dataset_info: `nabu.resources.dataset_analyzer.DatasetAnalyzer`
-        Dataset information structure
-    do_flatfield: If True apply flat field to compute the center of rotation
-    cor_options: optional dictionary that can contain the following keys:
-        * slice_idx: index of the slice to use for computing the sinogram (for sinogram based algorithms)
-        * subsampling subsampling
-        * radio_angles: angles of the radios to use (for radio based algorithms)
-    logger: logging object
-    """
     logger = LoggerOrPrint(logger)
     cor_options = cor_options or {}
     check_supported(method, list(cor_methods.keys()), "COR estimation method")
@@ -71,7 +56,6 @@ def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logg
             dataset_info,
             do_flatfield=do_flatfield,
             cor_options=cor_options,
-            radio_angles=cor_options.get("radio_angles", (0.0, np.pi)),
             logger=logger,
         )
         estimated_cor = cor_finder.find_cor()
@@ -82,7 +66,6 @@ def estimate_cor(method, dataset_info, do_flatfield=True, cor_options=None, logg
             slice_idx=cor_options.get("slice_idx", "middle"),
             subsampling=cor_options.get("subsampling", 10),
             do_flatfield=do_flatfield,
-            take_log=cor_options.get("take_log", True),
             cor_options=cor_options,
             logger=logger,
         )
@@ -197,12 +180,6 @@ class CORFinder(CORFinderBase):
         self._init_radios()
         self._apply_flatfield()
         self._apply_tilt()
-        # octave-accurate does not support half-acquisition scans,
-        # but information on field of view is only known here with the "dataset_info" object.
-        # Do the check here.
-        if self.dataset_info.is_halftomo and method == "octave-accurate":
-            raise ValueError("The CoR estimator 'octave-accurate' does not support half-acquisition scans")
-        #
 
     def _init_radios(self):
         self.radios, self._radios_indices = get_radio_pair(
@@ -243,13 +220,6 @@ 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 -----
-        # '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":
-            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)))
@@ -389,13 +359,7 @@ class SinoCORFinder(CORFinderBase):
 
         cor_exec_kwargs = update_func_kwargs(self.cor_finder.find_shift, self.cor_options)
         cor_exec_kwargs["return_relative_to_middle"] = False
-        # 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":
-            cor_exec_kwargs["side"] = self._lookup_side or "center"
-        #
+
         if self._lookup_side is not None:
             cor_exec_kwargs["side"] = self._lookup_side
 
@@ -490,7 +454,7 @@ class CompositeCORFinder(CORFinderBase):
         if (self.angle_max - self.angle_min) < 1.2 * np.pi:
             useful_span = None
             raise ValueError(
-                f"""Sinogram-based Center of Rotation estimation can only be used for scans over more than 180 degrees.
+                f"""Sinogram-based Center of Rotation estimation can only be used for scans over more than 180 degrees. 
                                  Your angular span was barely above 180 degrees, it was in fact {((self.angle_max - self.angle_min)/np.pi):.2f} x 180
                                  and it is not considered to be enough by the discriminating condition which requires at least 1.2 half-turns
                               """

{nabu-2024.2.0 → nabu-2024.2.0rc1}/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-2024.2.0rc1}/nabu/pipeline/tests/test_estimators.py

@@ -84,17 +84,13 @@ class TestCorNearPos:
 
     def test_cor_fourier_angles_standard(self):
         cor_options = extract_parameters(self.conf_std["reconstruction"].get("cor_options", None), sep=";")
-        # TODO modify test files
-        if "near_pos" in cor_options and "near" in cor_options.get("side", "") == "near":
-            cor_options["side"] = cor_options["near_pos"]
-        #
         for side in [None, "from_file", "center"]:
             if side is not None:
                 cor_options.update({"side": side})
             finder = SinoCORFinder("fourier-angles", self.ds_std, do_flatfield=True, cor_options=cor_options)
             cor = finder.find_cor()
             message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
-            assert np.isclose(self.true_cor + 0.5, cor, atol=self.abs_tol), message
+            assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message
 
     def test_cor_sliding_bliss(self):
         cor_options = extract_parameters(self.conf_bliss["reconstruction"].get("cor_options", None), sep=";")
@@ -118,4 +114,4 @@ class TestCorNearPos:
             finder = SinoCORFinder("fourier-angles", self.ds_bliss, do_flatfield=True, cor_options=cor_options)
             cor = finder.find_cor()
             message = f"Computed CoR {cor} and expected CoR {self.true_cor} do not coincide. Near_pos options was set to {cor_options.get('near_pos',None)}."
-            assert np.isclose(self.true_cor + 0.5, cor, atol=self.abs_tol), message
+            assert np.isclose(self.true_cor, cor, atol=self.abs_tol), message

{nabu-2024.2.0 → nabu-2024.2.0rc1}/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-2024.2.0rc1}/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]
@@ -409,13 +409,8 @@ class HDF5DatasetAnalyzer(DatasetAnalyzer):
         slices: list of slice
             A list where each item is a slice.
         """
-        name_to_attr = {
-            "projections": self.projections,
-            "flats": self.raw_flats,
-            "darks": self.raw_darks,
-        }
-        check_supported(what, name_to_attr.keys(), "image type")
-        images = name_to_attr[what]  # dict
+        check_supported(what, ["projections", "flats", "darks"], "image type")
+        images = getattr(self, what)  # dict
         # we can't directly use set() on slice() object (unhashable). Use tuples
         slices = set()
         for du in get_compacted_dataslices(images).values():

{nabu-2024.2.0 → nabu-2024.2.0rc1/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0
+Version: 2024.2.0rc1
 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-2024.2.0rc1}/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-2024.2.0rc1}/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",