nabu 2025.1.0.dev13__tar.gz → 2025.1.0rc1__tar.gz

{nabu-2025.1.0.dev13/nabu.egg-info → nabu-2025.1.0rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0.dev13
+Version: 2025.1.0rc1
 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>
@@ -14,7 +14,6 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -26,14 +25,14 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py>=3.0
 Requires-Dist: silx>=0.15.0
-Requires-Dist: tomoscan>=2.1.5
+Requires-Dist: tomoscan>=2.2.0a5
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2025.1.0-dev13"
+__version__ = "2025.1.0-rc1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/app/cast_volume.py

@@ -19,6 +19,7 @@ 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
@@ -109,7 +110,14 @@ def main(argv=None):
         default=None,
         help="Provide url to the histogram - like: '/{path}/my_file.hdf5?path/to/my/data' with my_file.hdf5 is the file containing the histogram. Located under 'path'. And 'path/to/my/data' is the location of the HDF5 dataset",
     )
-
+    parser.add_argument(
+        "--remove-input-volume",
+        "--remove",
+        dest="remove",
+        action="store_true",
+        default=False,
+        help="Whether to remove the input volume after cast. Default is False.",
+    )
     options = parser.parse_args(argv[1:])
 
     # handle input volume
@@ -270,6 +278,9 @@ def main(argv=None):
         rescale_min_percentile=rescale_min_percentile,
         rescale_max_percentile=rescale_max_percentile,
     )
+    if options.remove:
+        _logger.info(f"Removing {input_volume.data_url.file_path()}")
+        remove_volume(input_volume, check=True)
     exit(0)
 
 

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/app/cli_configs.py

@@ -8,6 +8,7 @@ from nabu.pipeline.config_validators import str2bool
 
 from tomoscan.framereducer.method import ReduceMethod
 
+reduce_methods = tuple(member.value for member in ReduceMethod)
 
 BootstrapConfig = {
     "bootstrap": {
@@ -162,7 +163,7 @@ MultiCorConfig = ReconstructConfig.copy()
 MultiCorConfig.update(
     {
         "cor": {
-            "help": "Positions of the center of rotation. It must be a list of comma-separated scalars, or in the form start:stop:step, where start, stop and step can all be floating-point values.",
+            "help": "Absolute positions of the center of rotation. It must be a list of comma-separated scalars, or in the form start:stop:step, where start, stop and step can all be floating-point values.",
             "default": "",
             "mandatory": True,
         },
@@ -322,6 +323,49 @@ CompareVolumesConfig = {
     },
 }
 
+EstimateMotionConfig = {
+    "dataset": {
+        "help": "Path to the dataset.",
+        "default": "",
+        "mandatory": True,
+    },
+    "flatfield": {
+        "help": "Whether to perform flatfield normalization. Default is True.",
+        "default": "1",
+        "type": int,
+    },
+    "rot_center": {
+        "help": "Center of rotation. If not provided, will be estimated.",
+        "default": None,
+    },
+    "subsampling": {
+        "help": "For 360-degrees scan, angular subsampling for matching opposite projections. Default is 10.",
+        "default": 10,
+        "type": int,
+    },
+    "deg_xy": {
+        "help": "Polynomial degree in x-y for sample movement polynomial model",
+        "default": 2,
+        "type": int,
+    },
+    "deg_z": {
+        "help": "Polynomial degree in z (vertical) for sample movement polynomial model",
+        "default": 2,
+        "type": int,
+    },
+    "verbose": {
+        "help": "Whether to plot the movement estimation fit",
+        "default": 1,
+    },
+    "output_file": {
+        "help": "Path of the output file containing the sample translations projected in the detector reference frame. This file can be directly used in 'translation_movements_file' of nabu configuration",
+        "default": "correct_motion.txt",
+    },
+    "only": {
+        "help": "Whether to only generate motion file for horizontal or vertical movement: --only horizontal  or --only vertical",
+        "default": "",
+    },
+}
 
 # Default configuration for "stitching" command
 StitchingConfig = {
@@ -344,7 +388,7 @@ StitchingConfig = {
 # Default configuration for "stitching-bootstrap" command
 BootstrapStitchingConfig = {
     "stitching-type": {
-        "help": f"User can provide stitching type to filter some parameters. Must be in {StitchingType.values()}.",
+        "help": f"User can provide stitching type to filter some parameters. Must be in {[sst for sst in StitchingType]}.",
         "default": None,
     },
     "level": {
@@ -559,12 +603,12 @@ ReduceDarkFlatConfig = {
         "required": False,
     },
     "dark-method": {
-        "help": f"Define the method to be used for computing darks. Valid methods are {ReduceMethod.values()}",
+        "help": f"Define the method to be used for computing darks. Valid methods are {reduce_methods}",
         "default": ReduceMethod.MEAN,
         "required": False,
     },
     "flat-method": {
-        "help": f"Define the method to be used for computing flats. Valid methods are {ReduceMethod.values()}",
+        "help": f"Define the method to be used for computing flats. Valid methods are {reduce_methods}",
         "default": ReduceMethod.MEDIAN,
         "required": False,
     },
@@ -608,6 +652,39 @@ ReduceDarkFlatConfig = {
     },
 }
 
+PCAFlatsConfig = {
+    "datasets": {"help": "datasets to be stitched together", "default": tuple(), "nargs": "+", "mandatory": True},
+    "flat-method": {
+        "help": f"Define the method to be used for computing flats. Valid methods are {reduce_methods}",
+        "default": ReduceMethod.MEDIAN,
+        "required": False,
+    },
+    "dark-method": {
+        "help": f"Define the method to be used for computing darks. Valid methods are {reduce_methods}",
+        "default": ReduceMethod.MEAN,
+        "required": False,
+    },
+    "overwrite": {
+        "dest": "overwrite",
+        "action": "store_true",
+        "default": False,
+        "help": "Overwrite dark/flats if exists",
+    },
+    "debug": {
+        "dest": "debug",
+        "action": "store_true",
+        "default": False,
+        "help": "Set logging system in debug mode",
+        "required": False,
+    },
+    "output-filename": {
+        "aliases": ("orfl",),
+        "default": None,
+        "help": "Where to save PCA flats. If not provided will be dumped in the current folder as{scan_prefix}_PCAFlats.hdf5",
+        "required": False,
+    },
+}
+
 ShowReconstructionTimingsConfig = {
     "logfile": {
         "help": "Path to the log file.",

nabu-2025.1.0rc1/nabu/app/estimate_motion.py

@@ -0,0 +1,54 @@
+from os import path
+
+from ..resources.nxflatfield import update_dataset_info_flats_darks
+from ..resources.logger import LoggerOrPrint
+from ..resources.dataset_analyzer import analyze_dataset
+from ..pipeline.config_validators import convert_to_bool
+from ..pipeline.estimators import TranslationsEstimator
+from .utils import parse_params_values
+from .cli_configs import EstimateMotionConfig
+
+
+def estimate_motion():
+    args = parse_params_values(
+        EstimateMotionConfig,
+        parser_description="Estimate sample motion and generate 'translation_movements_file' for nabu config file. ",
+    )
+    try:
+        rot_center = float(args["rot_center"])
+    except (ValueError, TypeError):
+        rot_center = None
+
+    logger = LoggerOrPrint(None)
+    dataset_info = analyze_dataset(args["dataset"], logger=logger)
+    do_ff = args["flatfield"]
+
+    if do_ff:
+        update_dataset_info_flats_darks(dataset_info, True, loading_mode="load_if_present")
+
+    est = TranslationsEstimator(
+        dataset_info,
+        do_flatfield=do_ff,
+        rot_center=rot_center,
+        angular_subsampling=args["subsampling"],
+        deg_xy=args["deg_xy"],
+        deg_z=args["deg_z"],
+        shifts_estimator="phase_cross_correlation",
+    )
+
+    estimated_shifts_h, estimated_shifts_v, cor = est.estimate_motion()
+    if convert_to_bool(args["verbose"]):
+        err_vu = est.motion_estimator.get_max_fit_error(cor=rot_center)
+        logger.info("Max fit error in 'u': %.2f pix \t\t Max fit error in 'v': %.2f pix" % (err_vu[1], err_vu[0]))
+        est.motion_estimator.plot_detector_shifts(cor=rot_center)
+        est.motion_estimator.plot_movements(cor=rot_center, angles_rad=dataset_info.rotation_angles)
+
+    out_file = args["output_file"]
+    est.generate_translations_movements_file(filename=out_file, only=args["only"] or None)
+    logger.info(
+        f"Wrote {out_file} - use 'translation_movements_file = {path.abspath(out_file)}' in nabu configuration file to correct for sample movements in the reconstruction'"
+    )
+
+
+if __name__ == "__main__":
+    estimate_motion()

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/app/multicor.py

@@ -34,16 +34,16 @@ def main():
         program_version="nabu " + version,
     )
 
+    cors = get_user_cors(args["cor"])
     reconstructor = get_reconstructor(
         args,
         # Put a dummy CoR to avoid crash in both full-FoV and extended-FoV.
         # It will be overwritten later by the user-defined CoRs
-        overwrite_options={"reconstruction/rotation_axis_position": 10.0},
+        overwrite_options={"reconstruction/rotation_axis_position": cors[0]},
     )
 
     if reconstructor.delta_z > 1:
         raise ValueError("Only slice reconstruction can be used (have delta_z = %d)" % reconstructor.delta_z)
-
     reconstructor.reconstruct()  # warm-up, spawn pipeline
 
     pipeline = reconstructor.pipeline
@@ -58,7 +58,6 @@ def main():
         pass
     ######
 
-    cors = get_user_cors(args["cor"])
     options = reconstructor.process_config.processing_options["reconstruction"]
     reconstruct_from_sinos_stack = (options["method"].lower() == "cone") or (
         options["method"].lower() == "mlem" and options["implementation"].lower() == "corrct"
@@ -81,7 +80,6 @@ def main():
         pipeline.processing_options["reconstruction"]["rotation_axis_position"] = cor
         pipeline.processing_options["save"]["file_prefix"] = file_prefix + "_%.03f" % cor
         pipeline._init_writer(create_subfolder=False, single_output_file_initialized=False)
-
         # Reconfigure center of rotation
         if not (do_halftomo):
             pipeline.reconstruction.reset_rot_center(cor)

nabu-2025.1.0rc1/nabu/app/pcaflats.py

@@ -0,0 +1,116 @@
+import sys
+import os
+import numpy as np
+import h5py
+from .utils import parse_params_values
+from ..utils import is_writeable
+from .cli_configs import PCAFlatsConfig
+from .. import version
+from ..preproc.flatfield import PCAFlatsDecomposer
+from ..io.reader import NXDarksFlats
+
+
+def get_flats_darks_in_nx(filename):
+    dfreader = NXDarksFlats(filename)
+    darks = np.concatenate([d for d in dfreader.get_raw_darks()], axis=0)
+    flats = np.concatenate([f for f in dfreader.get_raw_flats()], axis=0)
+    entry = dfreader.flats_reader.data_path.lstrip("/").split("/")[0]
+    return flats, darks, entry
+
+
+def get_flats_darks_from_h5(filename):
+    flats = []
+    darks = []
+    with h5py.File(filename, "r") as f:
+        for k, v in f.items():
+            if k == "1.1":
+                detector_name = decode_bytes(f["1.1/technique/tomoconfig/detector"][()][0])
+            else:
+                try:
+                    image_key = v["technique/image_key"][()]
+                except:
+                    raise NotImplementedError(
+                        "Legacy h5 file format is not handled. The entry of the h5 file should contain a 'technique/image_key' group."
+                    )
+                if image_key == 2:  # Darks
+                    darks.append(v[f"instrument/{detector_name}/data"][()])
+                elif image_key == 1:  # Flats
+                    flats.append(v[f"instrument/{detector_name}/data"][()])
+
+    flats = np.concatenate([f for f in flats], axis=0)
+    darks = np.concatenate([d for d in darks], axis=0)
+    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"):
+    """Compute the PCS decomposition of a series of flats and darks, possibly taken from various scans."""
+    try:
+        decomposer = PCAFlatsDecomposer(flats, darks)
+        decomposer.save_decomposition(pcaflats_filename, overwrite=overwrite, entry=entry)
+        success = True
+    except:
+        success = False
+        raise ValueError("An error occured in the PCA deccomposition.")
+    return success
+
+
+def decode_bytes(content):
+    if isinstance(content, bytes):
+        return content.decode()
+    else:
+        return content
+
+
+def main(argv=None):
+    """Compute PCA Flats on a series of datasets (h5 or NX)."""
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = parse_params_values(
+        PCAFlatsConfig,
+        parser_description=f"Compute a PCA Decomposition of flats acquired from various datasets..",
+        program_version="nabu " + version,
+        user_args=argv,
+    )
+
+    # Get "where to write".
+    abspath = os.path.abspath(args["output_filename"])
+    pcaflats_dir = os.path.dirname(abspath)
+    pcaflats_filename = os.path.basename(abspath)
+
+    if is_writeable(pcaflats_dir):
+        output_path = os.path.join(pcaflats_dir, pcaflats_filename)
+    else:
+        raise ValueError(f"Output dir {pcaflats_dir} is not writeable.")
+
+    # raise error if file exists and overwrite=False
+    if not args["overwrite"] and os.path.exists(output_path):
+        raise FileExistsError(f"Output file {output_path} already exists. Use --overwrite to overwrite it.")
+
+    # Collect raw darks and flats
+    flats_stack = []
+    darks_stack = []
+
+    for dataset in args["datasets"]:
+        filename = os.path.basename(dataset)
+        kind = filename.split(".")[-1]
+        if kind == "nx":
+            flats, darks, entry = get_flats_darks_in_nx(dataset)
+        elif kind in ("h5", "hdf5"):
+            flats, darks, entry = get_flats_darks_from_h5(dataset)
+
+        flats_stack.append(flats)
+        darks_stack.append(darks)
+
+    flats = np.concatenate(flats_stack, axis=0)
+    darks = np.concatenate(darks_stack, axis=0)
+
+    exit(
+        pcaflats_decomposition(
+            flats, darks, pcaflats_filename=args["output_filename"], overwrite=args["overwrite"], entry=entry
+        )
+    )
+
+
+if __name__ == "__main__":
+    main()

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/app/reconstruct.py

@@ -1,5 +1,5 @@
-from tomoscan.io import HDF5File
 from .. import version
+from ..io.reader import list_hdf5_entries
 from ..utils import list_match_queries
 from ..pipeline.config import parse_nabu_config_file
 from ..pipeline.config_validators import convert_to_int
@@ -92,12 +92,6 @@ def get_reconstructor(args, overwrite_options=None):
     return reconstructor
 
 
-def list_hdf5_entries(fname):
-    with HDF5File(fname, "r") as f:
-        entries = list(f.keys())
-    return entries
-
-
 def main():
     args = parse_params_values(
         ReconstructConfig,

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/app/reduce_dark_flat.py

@@ -12,6 +12,9 @@ from tomoscan.factory import Factory
 from silx.io.url import DataUrl
 
 
+reduce_methods = tuple(member.value for member in ReduceMethod)
+
+
 def _create_data_urls(output_file: Optional[str], output_data_path: Optional[str], name: str):
     """
     util function to compute reduced Data and metadata url(s)
@@ -65,8 +68,8 @@ def reduce_dark_flat(
     """
     calculation of the darks / flats calling tomoscan utils function
     """
-    dark_method = ReduceMethod.from_value(dark_method) if dark_method is not None else None
-    flat_method = ReduceMethod.from_value(flat_method) if flat_method is not None else None
+    dark_method = ReduceMethod(dark_method) if dark_method is not None else None
+    flat_method = ReduceMethod(flat_method) if flat_method is not None else None
 
     # 1. define url where to save the file
     ## 1.1 for darks

{nabu-2025.1.0.dev13 → nabu-2025.1.0rc1}/nabu/estimation/cor.py

@@ -132,7 +132,7 @@ class CenterOfRotation(AlignmentBase):
         img_2 = self._prepare_image(img_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
 
         cc = self._compute_correlation_fft(img_1, img_2, padding_mode, high_pass=high_pass, low_pass=low_pass)
-        img_shape = img_2.shape
+        img_shape = cc.shape  # Because cc.shape can differ from img_2.shape (e.g. in case of odd nb of cols)
         cc_vs = np.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
         cc_hs = np.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])