nabu 2024.2.14__tar.gz → 2025.1.0__tar.gz

{nabu-2024.2.14/nabu.egg-info → nabu-2025.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2024.2.14
+Version: 2025.1.0
 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>
@@ -14,24 +14,25 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Environment :: Console
 Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: >=3.7
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy<2,>1.9.0
+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>=2.2.2
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile
@@ -41,7 +42,6 @@ Requires-Dist: scikit-image; extra == "full"
 Requires-Dist: PyWavelets; extra == "full"
 Requires-Dist: glymur; extra == "full"
 Requires-Dist: pycuda!=2024.1.1; extra == "full"
-Requires-Dist: scikit-cuda; extra == "full"
 Requires-Dist: pycudwt; extra == "full"
 Requires-Dist: sluurp>=0.3; extra == "full"
 Requires-Dist: pyvkfft; extra == "full"

nabu-2025.1.0/doc/doc_config.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+from nabu.resources.nabu_config import nabu_config
+
+
+def generate(file_):
+    def write(content):
+        print(content, file=file_)
+    for section, values in nabu_config.items():
+        if section == "about":
+            continue
+        write("## %s\n" % section)
+        for key, val in values.items():
+            if val["type"] == "unsupported":
+                continue
+            write(val["help"] + "\n")
+            write(
+                "```ini\n%s = %s\n```"
+                % (key, val["default"])
+            )
+
+
+
+if __name__ == "__main__":
+
+    import sys, os
+    print(os.path.abspath(__file__))
+    exit(0)
+
+    fname = "/tmp/test.md"
+    with open(fname, "w") as f:
+        generate(f)

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.14"
+__version__ = "2025.1.0"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/app/bootstrap_stitching.py

@@ -23,12 +23,14 @@ def guess_tomo_objects(my_str: str) -> tuple:
     try:
         # create_tomo_object_from_identifier will raise an exception is the string does not match an identifier
         return (Factory.create_tomo_object_from_identifier(my_str),)
-    except Exception:
+    except Exception as exc:
+        print("Error:", str(exc))
         pass
 
     try:
         volumes = guess_volumes(my_str)
-    except Exception:
+    except Exception as exc:
+        print("Error:", str(exc))
         pass
     else:
         if len(volumes) > 0:

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/app/cast_volume.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 import argparse
 import os
 import sys
@@ -49,7 +46,7 @@ def main(argv=None):
 
     volume_help = f"""To define a volume you can either provide: \n
     * an url (recommanded way) - see details lower \n
-    * a path. For hdf5 and multitiff we expect a file path. For edf, tif and jp2k we expect a folder path. In this case we will try to deduce the Volume from it. \n 
+    * a path. For hdf5 and multitiff we expect a file path. For edf, tif and jp2k we expect a folder path. In this case we will try to deduce the Volume from it. \n
     url must be defined like: \n{_volume_url_helps}
     """
 
@@ -112,7 +109,14 @@ 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
@@ -150,16 +154,13 @@ def main(argv=None):
             except Exception as e:
                 raise ValueError(f"Fail to build output volume from {options.output_volume}") from e
 
+            # ruff: noqa: SIM102
             if output_format is not None:
                 if not (
-                    isinstance(output_volume, EDFVolume)
-                    and output_format == "edf"
-                    or isinstance(output_format, HDF5Volume)
-                    and output_format == "hdf5"
-                    or isinstance(output_format, JP2KVolume)
-                    and output_format == "jp2"
-                    or isinstance(output_format, (TIFFVolume, MultiTIFFVolume))
-                    and output_format == "tiff"
+                    (isinstance(output_volume, EDFVolume) and output_format == "edf")
+                    or (isinstance(output_format, HDF5Volume) and output_format == "hdf5")
+                    or (isinstance(output_format, JP2KVolume) and output_format == "jp2")
+                    or (isinstance(output_format, (TIFFVolume, MultiTIFFVolume)) and output_format == "tiff")
                 ):
                     raise ValueError(
                         "Requested 'output_type' and output volume url are incoherent. 'output_type' is optional when url provided"
@@ -264,7 +265,7 @@ def main(argv=None):
     # update output volume from options
     output_volume.overwrite = options.overwrite
     if options.compression_ratios is not None:
-        output_volume.cratios = list([int(value) for value in convert_str_to_tuple(options.compression_ratios)])
+        output_volume.cratios = [int(value) for value in convert_str_to_tuple(options.compression_ratios)]
 
     # do volume casting
     cast_volume(
@@ -275,6 +276,7 @@ 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,
     )
     exit(0)
 

{nabu-2024.2.14 → nabu-2025.1.0}/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 +323,64 @@ 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,
+    },
+    "win_size": {
+        "help": "Size of the look-up window for half-tomography",
+        "default": 300,
+        "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": "",
+    },
+    "ccd_filter_size": {
+        "help": "Size of conditional median filter to apply on radios. Default is zero (disabled)",
+        "default": 0,
+        "type": int,
+    },
+    "ccd_filter_threshold": {
+        "help": "Threshold for median filter, 'ccd_filter_size' is not zero. Default is 0.04",
+        "default": 0.04,
+        "type": float,
+    },
+}
 
 # Default configuration for "stitching" command
 StitchingConfig = {
@@ -344,7 +403,7 @@ 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": {
@@ -462,11 +521,6 @@ DiagToRotConfig = {
     "--diag_file": dict(
         required=True, help="The reconstruction file obtained by nabu-helical using the diag_zpro_run option", type=str
     ),
-    "--entry_name": dict(
-        required=False,
-        help="entry_name. Defauls is entry0000",
-        default="entry0000",
-    ),
     "--near": dict(
         required=False,
         help="This is a relative offset respect to the center of the radios. The cor will be searched around the provided value. If not given the optinal parameter original_scan must be the original nexus file; and the estimated core will be taken there. The netry_name parameter also must be provided in this case",
@@ -564,12 +618,12 @@ 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,
     },
@@ -613,6 +667,45 @@ 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,
+        "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-2024.2.14 → nabu-2025.1.0}/nabu/app/compare_volumes.py

@@ -61,7 +61,7 @@ def compare_volumes(fname1, fname2, h5_path, chunk_size, do_stats, stop_at_thres
     finally:
         f1.close()
         f2.close()
-        return result
+    return result
 
 
 def compare_volumes_cli():

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/app/composite_cor.py

@@ -1,14 +1,12 @@
-import logging
 import os
 import sys
 import numpy as np
 import re
 
 from nabu.resources.dataset_analyzer import HDF5DatasetAnalyzer
-from nabu.pipeline.estimators import CompositeCOREstimator, estimate_cor
+from nabu.pipeline.estimators import CompositeCOREstimator
 from nabu.resources.nxflatfield import update_dataset_info_flats_darks
 from nabu.resources.utils import extract_parameters
-from nxtomo.application.nxtomo import NXtomo
 from .. import version
 from .cli_configs import CompositeCorConfig
 from .utils import parse_params_values
@@ -24,7 +22,7 @@ class NumpyArrayEncoder(json.JSONEncoder):
 
 
 def main(user_args=None):
-    "Application to extract with the composite cor finder the center of rotation for a scan or a series of scans"
+    """Application to extract with the composite cor finder the center of rotation for a scan or a series of scans"""
 
     if user_args is None:
         user_args = sys.argv[1:]

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/app/diag_to_pix.py

@@ -31,7 +31,7 @@ from ..pipeline.estimators import oversample
   we must bring to the pixel size
 
   An example of collection is this :
-    
+
    |_____ diagnostics
    |               |  
                   |__ 0
@@ -72,10 +72,10 @@ def transform_images(diag, ovs):
 
 def detailed_merit(diag, shift):
     # res will become the merit summed over all the pairs theta, theta+180
-    res = 0.0
+    # res = 0.0
 
     # need to account for the weight also. So this will become the used weight for the pairs theta, theta+180
-    res_w = 0.0
+    # res_w = 0.0
 
     ## The following two variables are very important information to be collected.
     ## On the the z translation over a 360 turn
@@ -149,7 +149,7 @@ def build_total_merit_list(diag, oversample_factor, args):
     # calculats the merit at all the tested extra adjustment shifts.
 
     transform_images(diag, [oversample_factor, 1])
-    h_ima = diag.radios[0].shape[0]
+    # h_ima = diag.radios[0].shape[0]
     # search_radius_v = min(oversample_factor * args.search_radius_v, h_ima - 1)
     search_radius_v = oversample_factor * args.search_radius_v
 
@@ -233,7 +233,6 @@ def main(user_args=None):
     # For each key there is a sequence of radio, the corresponding sequence of weights map, the corresponding z translation, and angles
 
     zpix_mm = None
-    observed_oneturn_total_shift_zpix = None
 
     argument_list = [
         (DictToObj(h5todict(args.diag_file, os.path.join(diag_url, my_key))), oversample_factor, args)
@@ -244,7 +243,7 @@ def main(user_args=None):
     with Pool(processes=ncpus) as pool:
         all_res_plus_infos = pool.starmap(build_total_merit_list, argument_list)
 
-    observed_oneturn_total_shift_zpix, zpix_mm = None, None
+    _, zpix_mm = None, None
 
     # needs to flatten the result of pool.map
     for_all_pairs_detailed_merit_lists = []

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/app/diag_to_rot.py

@@ -31,7 +31,7 @@ from .cli_configs import DiagToRotConfig
   The collection is not done here. Here we exploit the result of a previous collection to deduce, looking at the correlations, the cor
 
   An example of collection is this :
-    
+
    |_____ diagnostics
    |               |  
                   |__ 0
@@ -68,7 +68,8 @@ def transform_images(diag, args):
     But beforehand it is beneficial to remove low spatial frequencies.
     And we do oversampling on the fly.
 
-    Parameters:
+    Parameters
+    ----------
        diag: object
          used member of diag are radios and weights
        args: object
@@ -196,7 +197,6 @@ def find_best_interpolating_line(args):
     z_b = np.nanmax(all_z_transl)
 
     best_error = np.nan
-    best_off_pair = None
 
     for index_ovlp_a in index_overlap_list_a:
         for index_ovlp_b in index_overlap_list_b:
@@ -204,7 +204,7 @@ def find_best_interpolating_line(args):
             indexes = (np.arange(all_energies.shape[0]))[~np.isnan(index_ovlps)].astype("i")
 
             index_ovlps = index_ovlps[~np.isnan(index_ovlps)]
-            index_ovlps = np.round_(index_ovlps).astype("i")
+            index_ovlps = np.round(index_ovlps).astype("i")
 
             diff_enes = all_res[(indexes, index_ovlps)]
             orig_enes = all_energies[(indexes, index_ovlps)]
@@ -313,13 +313,12 @@ def main(user_args=None):
             and this is not enough to do correlation + interpolation between sections
             """
             raise RuntimeError(message)
-    else:
-        if n_pairings_with_data < 1:
-            message = f""" The diagnostics collection has probably been run over a too thin section of the scan
+    elif n_pairings_with_data < 1:
+        message = f""" The diagnostics collection has probably been run over a too thin section of the scan
             or you scan does not allow to form pairs of theta, theta+360. I only found {n_pairings_with_data}
             pairings
             """
-            raise RuntimeError(message)
+        raise RuntimeError(message)
 
     # all_merits, all_energies, all_z_transls = zip( result_list )
 
@@ -345,15 +344,15 @@ def main(user_args=None):
 
 def do_height_by_height(args, overlap_list, all_diff, all_energies, all_z_transl):
     # now we find the best cor for each chunk, or nan if no overlap is found
-    z_a = np.min(all_z_transl)
-    z_b = np.max(all_z_transl)
+    # z_a = np.min(all_z_transl)
+    # z_b = np.max(all_z_transl)
 
     grouped_diff = {}
     grouped_energy = {}
 
     for diff, energy, z in zip(all_diff, all_energies, all_z_transl):
         found = z
-        for key in grouped_diff.keys():
+        for key in grouped_diff:
             if abs(key - z) < 2.0:  # these are in pixel units
                 found = key
                 break

{nabu-2024.2.14 → nabu-2025.1.0}/nabu/app/double_flatfield.py

@@ -11,14 +11,26 @@ from .utils import parse_params_values
 
 class DoubleFlatFieldChunks:
     def __init__(
-        self, dataset_path, output_file, chunk_size=100, sigma=None, do_flatfield=True, h5_entry=None, logger=None
+        self,
+        dataset_path,
+        output_file,
+        dataset_info=None,
+        chunk_size=100,
+        sigma=None,
+        do_flatfield=True,
+        h5_entry=None,
+        logger=None,
     ):
         self.logger = LoggerOrPrint(logger)
-        self.dataset_info = analyze_dataset(dataset_path, extra_options={"hdf5_entry": h5_entry}, logger=logger)
-        self.chunk_size = min(chunk_size, self.dataset_info.radio_dims[-1])
         self.do_flatfield = bool(do_flatfield)
-        if self.do_flatfield:
-            update_dataset_info_flats_darks(self.dataset_info, flatfield_mode=True)
+        if dataset_info is not None:
+            self.dataset_info = dataset_info
+        else:
+            self.dataset_info = analyze_dataset(dataset_path, extra_options={"hdf5_entry": h5_entry}, logger=logger)
+            if self.do_flatfield:
+                update_dataset_info_flats_darks(self.dataset_info, flatfield_mode=True)
+
+        self.chunk_size = min(chunk_size, self.dataset_info.radio_dims[-1])
         self.output_file = output_file
         self.sigma = sigma if sigma is not None and abs(sigma) > 1e-5 else None
 
@@ -103,6 +115,7 @@ class DoubleFlatFieldChunks:
         )
         writer.write(arr, "double_flatfield", config=self._get_config())
         self.logger.info("Wrote %s" % writer.fname)
+        return writer.fname
 
 
 def dff_cli():

nabu-2025.1.0/nabu/app/estimate_motion.py

@@ -0,0 +1,75 @@
+from os import path
+from multiprocessing.pool import ThreadPool
+
+from ..utils import get_num_threads
+from ..resources.nxflatfield import update_dataset_info_flats_darks
+from ..resources.logger import LoggerOrPrint
+from ..resources.dataset_analyzer import analyze_dataset
+from ..preproc.ccd import CCDFilter
+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")
+
+    radios_filter = None
+    do_ccd_filter = args["ccd_filter_size"] > 0
+    if do_ccd_filter:
+        radios_filter_obj = CCDFilter(
+            dataset_info.radio_dims[::-1],
+            kernel_size=args["ccd_filter_size"],
+            median_clip_thresh=args["ccd_filter_threshold"],
+        )
+
+        def radios_filter(images):
+            def _apply_median_clip(img):
+                radios_filter_obj.median_clip_correction(img, output=img)
+
+            with ThreadPool(get_num_threads()) as tp:
+                tp.map(_apply_median_clip, images)
+
+    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",
+        radios_filter=radios_filter,
+        extra_options={"window_size": args["win_size"]},
+    )
+
+    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()