nabu 2025.1.0.dev13__py3-none-any.whl → 2025.1.0rc1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nabu/__init__.py +1 -1
- nabu/app/cast_volume.py +12 -1
- nabu/app/cli_configs.py +81 -4
- nabu/app/estimate_motion.py +54 -0
- nabu/app/multicor.py +2 -4
- nabu/app/pcaflats.py +116 -0
- nabu/app/reconstruct.py +1 -7
- nabu/app/reduce_dark_flat.py +5 -2
- nabu/estimation/cor.py +1 -1
- nabu/estimation/motion.py +557 -0
- nabu/estimation/tests/test_motion_estimation.py +471 -0
- nabu/estimation/tilt.py +1 -1
- nabu/estimation/translation.py +47 -1
- nabu/io/cast_volume.py +94 -13
- nabu/io/reader.py +32 -1
- nabu/io/tests/test_remove_volume.py +152 -0
- nabu/pipeline/config_validators.py +42 -43
- nabu/pipeline/estimators.py +255 -0
- nabu/pipeline/fullfield/chunked.py +67 -43
- nabu/pipeline/fullfield/chunked_cuda.py +5 -2
- nabu/pipeline/fullfield/nabu_config.py +17 -11
- nabu/pipeline/fullfield/processconfig.py +8 -2
- nabu/pipeline/fullfield/reconstruction.py +3 -0
- nabu/pipeline/params.py +12 -0
- nabu/pipeline/tests/test_estimators.py +240 -3
- nabu/preproc/ccd.py +53 -3
- nabu/preproc/flatfield.py +306 -1
- nabu/preproc/shift.py +3 -1
- nabu/preproc/tests/test_pcaflats.py +154 -0
- nabu/processing/rotation_cuda.py +3 -1
- nabu/processing/tests/test_rotation.py +4 -2
- nabu/reconstruction/fbp.py +7 -0
- nabu/reconstruction/fbp_base.py +31 -7
- nabu/reconstruction/fbp_opencl.py +8 -0
- nabu/reconstruction/filtering_opencl.py +2 -0
- nabu/reconstruction/mlem.py +51 -14
- nabu/reconstruction/tests/test_filtering.py +13 -2
- nabu/reconstruction/tests/test_mlem.py +91 -62
- nabu/resources/dataset_analyzer.py +144 -20
- nabu/resources/nxflatfield.py +101 -35
- nabu/resources/tests/test_nxflatfield.py +1 -1
- nabu/resources/utils.py +16 -10
- nabu/stitching/alignment.py +7 -7
- nabu/stitching/config.py +22 -20
- nabu/stitching/definitions.py +2 -2
- nabu/stitching/overlap.py +4 -4
- nabu/stitching/sample_normalization.py +5 -5
- nabu/stitching/stitcher/post_processing.py +5 -3
- nabu/stitching/stitcher/pre_processing.py +24 -20
- nabu/stitching/tests/test_config.py +3 -3
- nabu/stitching/tests/test_y_preprocessing_stitching.py +11 -8
- nabu/stitching/tests/test_z_postprocessing_stitching.py +2 -2
- nabu/stitching/tests/test_z_preprocessing_stitching.py +23 -20
- nabu/stitching/utils/utils.py +7 -7
- nabu/testutils.py +1 -4
- nabu/utils.py +13 -0
- {nabu-2025.1.0.dev13.dist-info → nabu-2025.1.0rc1.dist-info}/METADATA +3 -4
- {nabu-2025.1.0.dev13.dist-info → nabu-2025.1.0rc1.dist-info}/RECORD +62 -57
- {nabu-2025.1.0.dev13.dist-info → nabu-2025.1.0rc1.dist-info}/WHEEL +1 -1
- {nabu-2025.1.0.dev13.dist-info → nabu-2025.1.0rc1.dist-info}/entry_points.txt +2 -1
- nabu/app/correct_rot.py +0 -62
- {nabu-2025.1.0.dev13.dist-info → nabu-2025.1.0rc1.dist-info}/licenses/LICENSE +0 -0
- {nabu-2025.1.0.dev13.dist-info → nabu-2025.1.0rc1.dist-info}/top_level.txt +0 -0
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nabu/__init__.py,sha256=
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nabu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/app/bootstrap.py,sha256=3yLZJmrmQBmPJMBtE2ih2cspfqOy5T_UN2U8B3i_hkI,3266
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nabu/app/cli_configs.py,sha256=D3KaMVnZ9eLnSzgSJmdNWhxF0GESbmXMYiNeOBzu1vY,24794
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nabu/app/estimate_motion.py,sha256=VyUv3scqbzj8mlccdMO3XgI-HIekFjxFtlVEGd2swo4,2079
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nabu/app/generate_header.py,sha256=Voo-FAvwS_mU5gtDxyqpZnSpP_mlMSfd_6bEtgdi_tg,8919
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nabu/stitching/tests/test_sample_normalization.py,sha256=a-F8geN8qrteDeQK37oeSYNdt49siyWFs3fZgPTRn4g,1328
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nabu/stitching/tests/test_slurm_utils.py,sha256=QTbtx5SRAK1JkbyI-GNSI5xeqVHI8KptD3STpOb09Pc,4951
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nabu/stitching/tests/test_utils.py,sha256=hIahPlogtnZNr_YkbN_Rcv-y6qG47IiRSSss51-cWK4,647
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nabu/stitching/tests/test_y_preprocessing_stitching.py,sha256=
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nabu/stitching/tests/test_z_postprocessing_stitching.py,sha256=
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nabu/stitching/tests/test_z_preprocessing_stitching.py,sha256=
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nabu/stitching/tests/test_y_preprocessing_stitching.py,sha256=9AGMM3glAVsZ-M1v-_DD1u_QWUb5Id5QldIOYnw-1vY,5179
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nabu/stitching/tests/test_z_postprocessing_stitching.py,sha256=vzWPGr2X-kN6WuRMHFMcEnSMjA9xv_TTq3pogpT8uEY,26908
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nabu/stitching/tests/test_z_preprocessing_stitching.py,sha256=aIaYaROpoMflx_wW-cOoLUqmngMEnRCXlQUuoGldcs4,16445
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nabu/stitching/utils/__init__.py,sha256=alIDGBnxWH4JvP-UW-7N99seBBi0r1GV1h8f1ERFBec,21
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nabu/stitching/utils/post_processing.py,sha256=aow36shbYhFgAnbCoq6mtXVpjBNCKm7VSLIvv3EYVdA,11303
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nabu/stitching/utils/utils.py,sha256=
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nabu/stitching/utils/utils.py,sha256=hX9WC-ZpmV31svQnKPO8Ek-uW-RZ3Ot4szfvuYpZjPg,24586
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nabu/stitching/utils/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/stitching/utils/tests/test_post-processing.py,sha256=X79gYJ2dwF_bjFWVQLu9odHNJaMmljfuI1-ROIp7jdE,766
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nabu/thirdparty/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -312,9 +317,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
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nabu/thirdparty/tomocupy_remove_stripe.py,sha256=Khe4zFf0kRzu65Yxnvq58gt1ljOztqJGdMDhVAiM7lM,24363
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nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
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nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
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nabu-2025.1.
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nabu-2025.1.0rc1.dist-info/licenses/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
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nabu-2025.1.0rc1.dist-info/METADATA,sha256=cm6lBb8UyHChthz3HLCNB8AojOzCX9ciK54SWWd2fGc,4276
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nabu-2025.1.0rc1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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nabu-2025.1.0rc1.dist-info/entry_points.txt,sha256=YxzCY5CNQ1XHrIGbRKg-BgC1Jy7QaCITdITpyhhxpZU,1338
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nabu-2025.1.0rc1.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
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nabu-2025.1.0rc1.dist-info/RECORD,,
|
@@ -8,12 +8,13 @@ nabu-diag2pix = nabu.app.diag_to_pix:main
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8
8
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nabu-diag2rot = nabu.app.diag_to_rot:main
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9
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nabu-display-timings = nabu.app.parse_reconstruction_log:parse_reclog_cli
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nabu-double-flatfield = nabu.app.double_flatfield:dff_cli
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nabu-estimate-motion = nabu.app.estimate_motion:estimate_motion
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nabu-generate-info = nabu.app.generate_header:generate_merged_info_file
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nabu-helical = nabu.app.reconstruct_helical:main_helical
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13
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-
nabu-helical-correct-rot = nabu.app.correct_rot:main
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14
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nabu-helical-prepare-weights-double = nabu.app.prepare_weights_double:main
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nabu-histogram = nabu.app.histogram:histogram_cli
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nabu-multicor = nabu.app.multicor:main
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nabu-pcaflats = nabu.app.pcaflats:main
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nabu-poly2map = nabu.app.create_distortion_map_from_poly:create_distortion_maps_entry_point
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nabu-reduce-dark-flat = nabu.app.reduce_dark_flat:main
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nabu-rotate = nabu.app.rotate:rotate_cli
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nabu/app/correct_rot.py
DELETED
@@ -1,62 +0,0 @@
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1
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-
from .. import version
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import sys
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import numpy as np
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from .utils import parse_params_values
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from .cli_configs import CorrectRotConfig
|
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from silx.io.dictdump import h5todict
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-
from nxtomo.application.nxtomo import NXtomo
|
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from nabu.utils import DictToObj
|
14
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-
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-
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def main(user_args=None):
|
17
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-
"""Applies the correction found by diag_to_rot to a nexus file"""
|
18
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-
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if user_args is None:
|
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user_args = sys.argv[1:]
|
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-
|
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|
-
args = DictToObj(
|
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|
-
parse_params_values(
|
24
|
-
CorrectRotConfig,
|
25
|
-
parser_description=main.__doc__,
|
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|
-
program_version="nabu " + version,
|
27
|
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user_args=user_args,
|
28
|
-
)
|
29
|
-
)
|
30
|
-
|
31
|
-
# now we read the results of the diag_to_rot utility, they are in the cor_file parameter
|
32
|
-
# of the cli
|
33
|
-
cor_data = DictToObj(h5todict(args.cor_file, "/"))
|
34
|
-
|
35
|
-
my_cor = cor_data.cor[0]
|
36
|
-
# we will take my_cor as cor at the first angular position
|
37
|
-
# and then we correct the x_translation at the other angles
|
38
|
-
|
39
|
-
# We now load the nexus that we wish to correct
|
40
|
-
nx_tomo = NXtomo().load(args.nexus_source, args.entry_name)
|
41
|
-
|
42
|
-
# The cor_file that we use for correction
|
43
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-
# is providing us with the z_m that gives for each
|
44
|
-
# cor position found in the cor array the corresponding value of
|
45
|
-
# the translation along z (in meters)
|
46
|
-
z_translation = nx_tomo.sample.z_translation.value
|
47
|
-
z_translation = z_translation - z_translation[0]
|
48
|
-
|
49
|
-
# now we interpolate to find the correction
|
50
|
-
# for each position of the encoders
|
51
|
-
cors = np.interp(z_translation, cor_data.z_m, cor_data.cor)
|
52
|
-
|
53
|
-
# this is the correction
|
54
|
-
x_correction = nx_tomo.instrument.detector.x_pixel_size.value * (cors - my_cor) # we are in meters here
|
55
|
-
|
56
|
-
# and we apply it to the nexus that we have loaded
|
57
|
-
nx_tomo.sample.x_translation = nx_tomo.sample.x_translation.value + x_correction
|
58
|
-
|
59
|
-
# finally we write it to the corrected nexus file
|
60
|
-
nx_tomo.save(file_path=args.nexus_target, data_path=args.entry_name, overwrite=True)
|
61
|
-
|
62
|
-
return 0
|
File without changes
|
File without changes
|