nabu 2025.1.0rc1__tar.gz → 2025.1.0rc3__tar.gz

{nabu-2025.1.0rc1/nabu.egg-info → nabu-2025.1.0rc3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc1
+Version: 2025.1.0rc3
 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>
@@ -32,7 +32,7 @@ Requires-Dist: numpy>1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py>=3.0
 Requires-Dist: silx>=0.15.0
-Requires-Dist: tomoscan>=2.2.0a5
+Requires-Dist: tomoscan>=2.2.2
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2025.1.0-rc1"
+__version__ = "2025.1.0-rc3"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/app/cast_volume.py

@@ -19,7 +19,6 @@ from nabu.io.cast_volume import (
     RESCALE_MIN_PERCENTILE,
     cast_volume,
     get_default_output_volume,
-    remove_volume,
 )
 from nabu.pipeline.params import files_formats
 from nabu.utils import convert_str_to_tuple
@@ -277,10 +276,8 @@ def main(argv=None):
         data_max=data_max,
         rescale_min_percentile=rescale_min_percentile,
         rescale_max_percentile=rescale_max_percentile,
+        remove_input_volume=options.remove,
     )
-    if options.remove:
-        _logger.info(f"Removing {input_volume.data_url.file_path()}")
-        remove_volume(input_volume, check=True)
     exit(0)
 
 

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/app/cli_configs.py

@@ -654,6 +654,12 @@ ReduceDarkFlatConfig = {
 
 PCAFlatsConfig = {
     "datasets": {"help": "datasets to be stitched together", "default": tuple(), "nargs": "+", "mandatory": True},
+    "nsigma": {
+        "help": "Paramter to select PCA components. Default is 3. Higher nsigma, less components.",
+        "default": 3.0,
+        "type": float,
+        "required": False,
+    },
     "flat-method": {
         "help": f"Define the method to be used for computing flats. Valid methods are {reduce_methods}",
         "default": ReduceMethod.MEDIAN,

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/app/pcaflats.py

@@ -42,10 +42,12 @@ def get_flats_darks_from_h5(filename):
     return flats, darks, "entry0000"  # TODO this will be problematic on the reconstruction side
 
 
-def pcaflats_decomposition(flats, darks, pcaflats_filename="PCAFlats.h5", overwrite=False, entry="entry0000"):
+def pcaflats_decomposition(
+    flats, darks, pcaflats_filename="PCAFlats.h5", overwrite=False, entry="entry0000", nsigma=3.0
+):
     """Compute the PCS decomposition of a series of flats and darks, possibly taken from various scans."""
     try:
-        decomposer = PCAFlatsDecomposer(flats, darks)
+        decomposer = PCAFlatsDecomposer(flats, darks, nsigma=nsigma)
         decomposer.save_decomposition(pcaflats_filename, overwrite=overwrite, entry=entry)
         success = True
     except:
@@ -74,7 +76,11 @@ def main(argv=None):
     )
 
     # Get "where to write".
-    abspath = os.path.abspath(args["output_filename"])
+    if args["output_filename"] is None:
+        abspath = os.path.abspath("./PCAFlats.hdf5")
+    else:
+        abspath = os.path.abspath(args["output_filename"])
+
     pcaflats_dir = os.path.dirname(abspath)
     pcaflats_filename = os.path.basename(abspath)
 
@@ -107,7 +113,7 @@ def main(argv=None):
 
     exit(
         pcaflats_decomposition(
-            flats, darks, pcaflats_filename=args["output_filename"], overwrite=args["overwrite"], entry=entry
+            flats, darks, pcaflats_filename=output_path, overwrite=args["overwrite"], entry=entry, nsigma=args["nsigma"]
         )
     )
 

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/cuda/src/backproj.cu

@@ -132,10 +132,10 @@ __global__ void backproj(
         sum3 += tex2D(tex_projections, h3 + 0.5f, proj + 0.5f);
         sum4 += tex2D(tex_projections, h4 + 0.5f, proj + 0.5f);
         #else
-        sum1 += linear_interpolation(d_sino, num_bins, h1, proj);
-        sum2 += linear_interpolation(d_sino, num_bins, h2, proj);
-        sum3 += linear_interpolation(d_sino, num_bins, h3, proj);
-        sum4 += linear_interpolation(d_sino, num_bins, h4, proj);
+        if (h1 >= 0 && h1 < num_bins) sum1 += linear_interpolation(d_sino, num_bins, h1, proj);
+        if (h2 >= 0 && h2 < num_bins) sum2 += linear_interpolation(d_sino, num_bins, h2, proj);
+        if (h3 >= 0 && h3 < num_bins) sum3 += linear_interpolation(d_sino, num_bins, h3, proj);
+        if (h4 >= 0 && h4 < num_bins) sum4 += linear_interpolation(d_sino, num_bins, h4, proj);
         #endif
     }
 

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/io/cast_volume.py

@@ -139,6 +139,7 @@ def cast_volume(
     rescale_max_percentile=RESCALE_MAX_PERCENTILE,
     save=True,
     store=False,
+    remove_input_volume: bool = False,
 ) -> VolumeBase:
     """
     cast givent volume to output_volume of 'output_data_type' type
@@ -248,6 +249,14 @@ def cast_volume(
     except (OSError, KeyError):
         # if no metadata provided and or saved in disk or if some key are missing
         pass
+
+    if save and output_volume.metadata is not None:
+        output_volume.save_metadata()
+
+    if remove_input_volume:
+        _logger.info(f"Removing {input_volume.data_url.file_path()}")
+        remove_volume(input_volume, check=True)
+
     return output_volume
 
 

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/opencl/src/backproj.cl

@@ -116,10 +116,10 @@ kernel void backproj(
         sum3 += read_imagef(d_sino, sampler, (float2) (h3 +0.5f,proj +0.5f)).x;
         sum4 += read_imagef(d_sino, sampler, (float2) (h4 +0.5f,proj +0.5f)).x;
         #else
-        sum1 += linear_interpolation(d_sino, num_bins, h1, proj);
-        sum2 += linear_interpolation(d_sino, num_bins, h2, proj);
-        sum3 += linear_interpolation(d_sino, num_bins, h3, proj);
-        sum4 += linear_interpolation(d_sino, num_bins, h4, proj);
+        if (h1 >= 0 && h1 < num_bins) sum1 += linear_interpolation(d_sino, num_bins, h1, proj);
+        if (h2 >= 0 && h2 < num_bins) sum2 += linear_interpolation(d_sino, num_bins, h2, proj);
+        if (h3 >= 0 && h3 < num_bins) sum3 += linear_interpolation(d_sino, num_bins, h3, proj);
+        if (h4 >= 0 && h4 < num_bins) sum4 += linear_interpolation(d_sino, num_bins, h4, proj);
         #endif
     }
 

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/pipeline/fullfield/nabu_config.py

@@ -16,9 +16,9 @@ nabu_config = {
             "type": "advanced",
         },
         "nexus_version": {
-            "default": "1.4",
-            "help": "Nexus version to use when browsing the HDF5 dataset. Default is 1.0.",
-            "validator": float_validator,
+            "default": "",
+            "help": "Specify a Nexus version to use when browsing the HDF5 dataset.",
+            "validator": optional_float_validator,
             "type": "advanced",
         },
         "darks_flats_dir": {

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/pipeline/fullfield/processconfig.py

@@ -4,7 +4,7 @@ import numpy as np
 from .get_double_flatfield import get_double_flatfield
 from silx.io import get_data
 from silx.io.url import DataUrl
-from ...utils import copy_dict_items, compare_dicts
+from ...utils import copy_dict_items, compare_dicts, deprecation_warning
 from ...io.utils import hdf5_entry_exists, get_h5_value
 from ...io.reader import import_h5_to_dict
 from ...resources.utils import extract_parameters, get_values_from_file
@@ -86,8 +86,6 @@ class ProcessConfig(ProcessConfigBase):
         elif self.dataset_info.kind == "edf":
             self.dataset_info.flats = self.dataset_info.get_reduced_flats()
             self.dataset_info.darks = self.dataset_info.get_reduced_darks()
-        else:
-            raise TypeError("Unknown dataset format")
         self.rec_params = self.nabu_config["reconstruction"]
 
         subsampling_factor, subsampling_start = self.nabu_config["dataset"]["projections_subsampling"]
@@ -476,6 +474,14 @@ class ProcessConfig(ProcessConfigBase):
         #
         # Double flat field
         #
+        # ---- COMPAT  ----
+        if nabu_config["preproc"].get("double_flatfield_enabled", False):
+            deprecation_warning(
+                "'double_flatfield_enabled' has been renamed to 'double_flatfield'. Please update your configuration file"
+            )
+            nabu_config["preproc"]["double_flatfield"] = True
+
+        # -------------
         if nabu_config["preproc"]["double_flatfield"]:
             tasks.append("double_flatfield")
             options["double_flatfield"] = {

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/pipeline/fullfield/reconstruction.py

@@ -486,7 +486,7 @@ class FullFieldReconstructor:
                 {
                     "sub_region": (
                         (0, self.n_angles),
-                        (curr_z_min - margin_up, curr_z_max + margin_down),
+                        (int(curr_z_min - margin_up), int(curr_z_max + margin_down)),
                         (0, self.chunk_shape[-1]),
                     ),
                     "margin": ((margin_up, margin_down), (0, 0)),

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/preproc/ccd.py

@@ -167,7 +167,7 @@ class CCDFilter:
             med = self.median_filter(dimg, self.kernel_size)
             err = dimg - med
             ds0 = err.std()
-            msk = err > ds0 * nsigma
+            msk = err > (ds0 * nsigma)
             gromsk = binary_dilation(msk)
 
             output[i] = np.where(gromsk, med, radios[i])

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu/preproc/flatfield.py

@@ -669,7 +669,7 @@ class PCAFlatsDecomposer:
     def _ccdfilter_and_log(self, flats: np.ndarray):
         """Dezinger (substract dark, apply median filter) and takes log of the flat stack"""
 
-        self.ccdfilter.dezinger_correction(flats, self.dark, nsigma=self.nsigma)
+        self.ccdfilter.dezinger_correction(flats, self.dark)
 
         with ThreadPool(self.n_threads) as tp:
             for i, frame in enumerate(tp.map(np.log, flats)):

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc1
+Version: 2025.1.0rc3
 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>
@@ -32,7 +32,7 @@ Requires-Dist: numpy>1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py>=3.0
 Requires-Dist: silx>=0.15.0
-Requires-Dist: tomoscan>=2.2.0a5
+Requires-Dist: tomoscan>=2.2.2
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/nabu.egg-info/requires.txt

@@ -2,7 +2,7 @@ numpy>1.9.0
 scipy
 h5py>=3.0
 silx>=0.15.0
-tomoscan>=2.2.0a5
+tomoscan>=2.2.2
 psutil
 pytest
 tifffile

{nabu-2025.1.0rc1 → nabu-2025.1.0rc3}/pyproject.toml

@@ -54,7 +54,7 @@ dependencies = [
     "scipy",
     "h5py>=3.0",
     "silx >= 0.15.0",
-    "tomoscan >= 2.2.0a5",
+    "tomoscan >= 2.2.2",
     "psutil",
     "pytest",
     "tifffile",