tomwer 1.4.5__py3-none-any.whl → 1.4.7__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.
- orangecontrib/tomwer/__init__.py +4 -0
- orangecontrib/tomwer/tests/TestAcquisition.py +1 -3
- orangecontrib/tomwer/widgets/__init__.py +3 -23
- orangecontrib/tomwer/widgets/cluster/__init__.py +3 -23
- orangecontrib/tomwer/widgets/control/__init__.py +4 -23
- orangecontrib/tomwer/widgets/dataportal/__init__.py +5 -0
- orangecontrib/tomwer/widgets/debugtools/__init__.py +3 -23
- orangecontrib/tomwer/widgets/edit/__init__.py +3 -23
- orangecontrib/tomwer/widgets/other/__init__.py +3 -23
- orangecontrib/tomwer/widgets/reconstruction/__init__.py +3 -23
- orangecontrib/tomwer/widgets/stitching/__init__.py +4 -0
- orangecontrib/tomwer/widgets/visualization/__init__.py +3 -23
- tomwer/__init__.py +2 -1
- tomwer/app/__init__.py +1 -2
- tomwer/app/axis.py +1 -2
- tomwer/app/canvas.py +1 -2
- tomwer/app/diffframe.py +1 -2
- tomwer/app/imagekeyeditor.py +1 -2
- tomwer/app/imagekeyupgrader.py +1 -2
- tomwer/app/multicor.py +1 -2
- tomwer/app/multipag.py +1 -2
- tomwer/app/nabuapp.py +1 -2
- tomwer/app/nxtomoeditor.py +1 -2
- tomwer/app/patchrawdarkflat.py +1 -2
- tomwer/app/radiostack.py +1 -2
- tomwer/app/reducedarkflat.py +1 -2
- tomwer/app/samplemoved.py +1 -2
- tomwer/app/scanviewer.py +1 -2
- tomwer/app/sinogramviewer.py +1 -2
- tomwer/core/__init__.py +1 -2
- tomwer/core/cluster/__init__.py +1 -2
- tomwer/core/futureobject.py +1 -2
- tomwer/core/log/__init__.py +1 -2
- tomwer/core/process/cluster/supervisor.py +1 -2
- tomwer/core/process/reconstruction/axis/axis.py +1 -2
- tomwer/core/process/reconstruction/nabu/nabucommon.py +6 -5
- tomwer/core/process/reconstruction/saaxis/saaxis.py +1 -2
- tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +1 -2
- tomwer/core/utils/__init__.py +1 -2
- tomwer/core/utils/image.py +2 -2
- tomwer/gui/cluster/__init__.py +1 -2
- tomwer/gui/conditions/__init__.py +1 -2
- tomwer/gui/configuration/__init__.py +1 -2
- tomwer/gui/control/__init__.py +1 -2
- tomwer/gui/dataportal/__init__.py +1 -2
- tomwer/gui/debugtools/__init__.py +1 -2
- tomwer/gui/dialog/QDataDialog.py +1 -2
- tomwer/gui/dialog/QVolumeDialog.py +1 -2
- tomwer/gui/edit/__init__.py +1 -2
- tomwer/gui/imagefromfile.py +1 -2
- tomwer/gui/metadataloader.py +1 -2
- tomwer/gui/qconfigfile.py +1 -2
- tomwer/gui/qlefilesystem.py +1 -2
- tomwer/gui/reconstruction/__init__.py +1 -2
- tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +3 -2
- tomwer/gui/reconstruction/nabu/slices.py +3 -3
- tomwer/gui/settings.py +1 -2
- tomwer/gui/stackplot.py +1 -2
- tomwer/gui/stitching/__init__.py +1 -2
- tomwer/gui/utils/slider.py +1 -2
- tomwer/gui/visualization/__init__.py +1 -2
- tomwer/io/__init__.py +1 -2
- tomwer/version.py +1 -1
- {tomwer-1.4.5.dist-info → tomwer-1.4.7.dist-info}/METADATA +4 -3
- {tomwer-1.4.5.dist-info → tomwer-1.4.7.dist-info}/RECORD +69 -70
- {tomwer-1.4.5.dist-info → tomwer-1.4.7.dist-info}/WHEEL +1 -1
- orangecontrib/tomwer/tutorials/test_cor.ows +0 -19
- {tomwer-1.4.5.dist-info → tomwer-1.4.7.dist-info}/LICENSE +0 -0
- {tomwer-1.4.5.dist-info → tomwer-1.4.7.dist-info}/entry_points.txt +0 -0
- {tomwer-1.4.5.dist-info → tomwer-1.4.7.dist-info}/top_level.txt +0 -0
orangecontrib/tomwer/__init__.py
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(Ewoks)Orange Widgets dedicated for tomography
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"""
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"""
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(Ewoks)Orange Widgets for remote processing through slurm
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"""
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"""
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(Ewoks)Orange Widgets to 'control' the flow. Like defining input / output, stacking scans...
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Those widget are not doing any 'core' processing.
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"""
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NAME = "control"
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"""
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(Ewoks)Orange Widgets for debugging. To be used at your own risk and peril
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"""
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NAME = "debug tools"
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"""
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(Ewoks)Orange Widgets for NXtomo edition
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"""
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NAME = "edit HDF5 - NXTomo"
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"""
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(Ewoks)Orange Widgets for tomography not matching any other category
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"""
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(Ewoks)Orange Widgets for tomography core processing
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"""
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NAME = "reconstruction"
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(Ewoks)Orange Widgets for tomography raw and processed data visualization
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tomwer/__init__.py
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tomwer/app/__init__.py
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"""This package contains all the applications that can be launched from 'tomwer'
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"""This package contains all the applications that can be launched from 'tomwer'"""
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"""Application to edit (key by key) the 'imagekey' value of a NXtomo ('imagekey' defines if a frame is a 'dark', 'flat' or a 'projection')
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"""Application to edit (key by key) the 'imagekey' value of a NXtomo ('imagekey' defines if a frame is a 'dark', 'flat' or a 'projection')"""
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"""Application to reconstruct a slice for a set of center of rotation value. Interface to nabu multicor
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"""Application to reconstruct a slice for a set of center of rotation value. Interface to nabu multicor"""
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"""Application to reconstruct a slice with Paganin for a set of delta/beta values.
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"""Application to reconstruct a slice with Paganin for a set of delta/beta values."""
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"""Application to display a couple of projections at 180 degree and estimate (by eye) if a sample has moved
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|
-
"""
|
3
|
+
"""Application to display a couple of projections at 180 degree and estimate (by eye) if a sample has moved"""
|
5
4
|
|
6
5
|
import argparse
|
7
6
|
import logging
|
tomwer/app/scanviewer.py
CHANGED
tomwer/app/sinogramviewer.py
CHANGED
tomwer/core/__init__.py
CHANGED
@@ -1,2 +1 @@
|
|
1
|
-
"""This package contains all the core functions / classes of tomwer
|
2
|
-
"""
|
1
|
+
"""This package contains all the core functions / classes of tomwer"""
|
tomwer/core/cluster/__init__.py
CHANGED
tomwer/core/futureobject.py
CHANGED
@@ -1,5 +1,4 @@
|
|
1
|
-
"""contains 'FutureTomwerObject'. Class used when computation is done asynchronously (when submitted to slurm for example)
|
2
|
-
"""
|
1
|
+
"""contains 'FutureTomwerObject'. Class used when computation is done asynchronously (when submitted to slurm for example)"""
|
3
2
|
|
4
3
|
from __future__ import annotations
|
5
4
|
|
tomwer/core/log/__init__.py
CHANGED
@@ -1,2 +1 @@
|
|
1
|
-
"""contains some log utils (used to notify processing advancement)
|
2
|
-
"""
|
1
|
+
"""contains some log utils (used to notify processing advancement)"""
|
@@ -1,5 +1,4 @@
|
|
1
|
-
"""contain utils for score process
|
2
|
-
"""
|
1
|
+
"""contain utils for score process"""
|
3
2
|
|
4
3
|
from __future__ import annotations
|
5
4
|
|
@@ -414,10 +413,12 @@ class _NabuBaseReconstructor:
|
|
414
413
|
:return: results of the slurm run
|
415
414
|
"""
|
416
415
|
if not isinstance(conf_file, str):
|
417
|
-
raise TypeError(
|
416
|
+
raise TypeError(
|
417
|
+
f"conf_file is expected to be a string not {type(conf_file)}"
|
418
|
+
)
|
418
419
|
if not isinstance(config_to_dump, dict):
|
419
420
|
raise TypeError(
|
420
|
-
f"config_to_dump is expected to be a
|
421
|
+
f"config_to_dump is expected to be a string not {type(config_to_dump)}"
|
421
422
|
)
|
422
423
|
if not is_slurm_available():
|
423
424
|
raise RuntimeError("slurm not available")
|
@@ -450,7 +451,7 @@ class _NabuBaseReconstructor:
|
|
450
451
|
job = SBatchScriptJob(
|
451
452
|
slurm_config=cluster_config,
|
452
453
|
script=(
|
453
|
-
f"python3 -m {settings.NABU_FULL_FIELD_APP_PATH} {conf_file} --gpu_mem_fraction {gpu_mem_fraction} --cpu_mem_fraction {cpu_mem_fraction}",
|
454
|
+
f"python3 -m {settings.NABU_FULL_FIELD_APP_PATH} '{conf_file}' --gpu_mem_fraction {gpu_mem_fraction} --cpu_mem_fraction {cpu_mem_fraction}",
|
454
455
|
),
|
455
456
|
script_path=os.path.join(self.scan.path, "slurm_scripts", script_name),
|
456
457
|
clean_script=False,
|
tomwer/core/utils/__init__.py
CHANGED
@@ -1,2 +1 @@
|
|
1
|
-
"""Several core utils
|
2
|
-
"""
|
1
|
+
"""Several core utils"""
|
tomwer/core/utils/image.py
CHANGED
@@ -116,8 +116,8 @@ def scale_img2_to_img1(
|
|
116
116
|
else:
|
117
117
|
raise ValueError("method not managed", method)
|
118
118
|
|
119
|
-
vec0 = numpy.
|
120
|
-
matr = numpy.
|
119
|
+
vec0 = numpy.asmatrix([[min0], [me0], [max0]])
|
120
|
+
matr = numpy.asmatrix(
|
121
121
|
[[min1 * min1, min1, 1.0], [me1 * me1, me1, 1.0], [max1 * max1, max1, 1.0]]
|
122
122
|
)
|
123
123
|
vec1 = inv(matr) * vec0
|
tomwer/gui/cluster/__init__.py
CHANGED
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets for remote processing
|
2
|
-
"""
|
1
|
+
"""Widgets for remote processing"""
|
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets for conditions (filters to let a scan continue processing or not)
|
2
|
-
"""
|
1
|
+
"""Widgets for conditions (filters to let a scan continue processing or not)"""
|
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets to define the configuration level we want to display (display only basic configuration/settings, advance...)
|
2
|
-
"""
|
1
|
+
"""Widgets to define the configuration level we want to display (display only basic configuration/settings, advance...)"""
|
tomwer/gui/control/__init__.py
CHANGED
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets related to 'control' tasks (select a scan, convert a scan with nxtomomill...)
|
2
|
-
"""
|
1
|
+
"""Widgets related to 'control' tasks (select a scan, convert a scan with nxtomomill...)"""
|
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets related to icat / drac
|
2
|
-
"""
|
1
|
+
"""Widgets related to icat / drac"""
|
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets useful to debut a tomography workflow (generate random scan...)
|
2
|
-
"""
|
1
|
+
"""Widgets useful to debut a tomography workflow (generate random scan...)"""
|
tomwer/gui/dialog/QDataDialog.py
CHANGED
tomwer/gui/edit/__init__.py
CHANGED
@@ -1,2 +1 @@
|
|
1
|
-
"""Widgets related to 'control' tasks (select a scan, convert a scan with nxtomomill...)
|
2
|
-
"""
|
1
|
+
"""Widgets related to 'control' tasks (select a scan, convert a scan with nxtomomill...)"""
|
tomwer/gui/imagefromfile.py
CHANGED
tomwer/gui/metadataloader.py
CHANGED
tomwer/gui/qconfigfile.py
CHANGED