nabu 2024.1.9__py3-none-any.whl → 2024.2.0__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/bootstrap.py +2 -3
- nabu/app/cast_volume.py +4 -2
- nabu/app/cli_configs.py +5 -0
- nabu/app/composite_cor.py +1 -1
- nabu/app/create_distortion_map_from_poly.py +5 -6
- nabu/app/diag_to_pix.py +7 -19
- nabu/app/diag_to_rot.py +14 -29
- nabu/app/double_flatfield.py +32 -44
- nabu/app/parse_reconstruction_log.py +3 -0
- nabu/app/reconstruct.py +53 -15
- nabu/app/reconstruct_helical.py +2 -2
- nabu/app/stitching.py +27 -13
- nabu/app/tests/test_reduce_dark_flat.py +4 -1
- nabu/cuda/kernel.py +11 -2
- nabu/cuda/processing.py +2 -2
- nabu/cuda/src/cone.cu +77 -0
- nabu/cuda/src/hierarchical_backproj.cu +271 -0
- nabu/cuda/utils.py +0 -6
- nabu/estimation/alignment.py +5 -19
- nabu/estimation/cor.py +173 -599
- nabu/estimation/cor_sino.py +356 -26
- nabu/estimation/focus.py +63 -11
- nabu/estimation/tests/test_cor.py +124 -58
- nabu/estimation/tests/test_focus.py +6 -6
- nabu/estimation/tilt.py +2 -1
- nabu/estimation/utils.py +5 -33
- nabu/io/__init__.py +1 -1
- nabu/io/cast_volume.py +1 -1
- nabu/io/reader.py +416 -21
- nabu/io/tests/test_readers.py +422 -0
- nabu/io/tests/test_writers.py +1 -102
- nabu/io/writer.py +4 -433
- nabu/opencl/kernel.py +14 -3
- nabu/opencl/processing.py +8 -0
- nabu/pipeline/config_validators.py +5 -2
- nabu/pipeline/datadump.py +12 -5
- nabu/pipeline/estimators.py +162 -188
- nabu/pipeline/fullfield/chunked.py +168 -92
- nabu/pipeline/fullfield/chunked_cuda.py +7 -3
- nabu/pipeline/fullfield/computations.py +2 -7
- nabu/pipeline/fullfield/dataset_validator.py +0 -4
- nabu/pipeline/fullfield/nabu_config.py +37 -13
- nabu/pipeline/fullfield/processconfig.py +22 -13
- nabu/pipeline/fullfield/reconstruction.py +13 -9
- nabu/pipeline/helical/helical_chunked_regridded.py +1 -1
- nabu/pipeline/helical/helical_chunked_regridded_cuda.py +1 -0
- nabu/pipeline/helical/helical_reconstruction.py +1 -1
- nabu/pipeline/params.py +21 -1
- nabu/pipeline/processconfig.py +1 -12
- nabu/pipeline/reader.py +146 -0
- nabu/pipeline/tests/test_estimators.py +44 -72
- nabu/pipeline/utils.py +4 -2
- nabu/pipeline/writer.py +10 -2
- nabu/preproc/ccd_cuda.py +1 -1
- nabu/preproc/ctf.py +14 -7
- nabu/preproc/ctf_cuda.py +2 -3
- nabu/preproc/double_flatfield.py +5 -12
- nabu/preproc/double_flatfield_cuda.py +2 -2
- nabu/preproc/flatfield.py +5 -1
- nabu/preproc/flatfield_cuda.py +5 -1
- nabu/preproc/phase.py +24 -73
- nabu/preproc/phase_cuda.py +5 -8
- nabu/preproc/tests/test_ctf.py +11 -7
- nabu/preproc/tests/test_flatfield.py +67 -122
- nabu/preproc/tests/test_paganin.py +54 -30
- nabu/processing/azim.py +206 -0
- nabu/processing/convolution_cuda.py +1 -1
- nabu/processing/fft_cuda.py +15 -17
- nabu/processing/histogram.py +2 -0
- nabu/processing/histogram_cuda.py +2 -1
- nabu/processing/kernel_base.py +3 -0
- nabu/processing/muladd_cuda.py +1 -0
- nabu/processing/padding_opencl.py +1 -1
- nabu/processing/roll_opencl.py +1 -0
- nabu/processing/rotation_cuda.py +2 -2
- nabu/processing/tests/test_fft.py +17 -10
- nabu/processing/unsharp_cuda.py +1 -1
- nabu/reconstruction/cone.py +104 -40
- nabu/reconstruction/fbp.py +3 -0
- nabu/reconstruction/fbp_base.py +7 -2
- nabu/reconstruction/filtering.py +20 -7
- nabu/reconstruction/filtering_cuda.py +7 -1
- nabu/reconstruction/hbp.py +424 -0
- nabu/reconstruction/mlem.py +99 -0
- nabu/reconstruction/reconstructor.py +2 -0
- nabu/reconstruction/rings_cuda.py +19 -19
- nabu/reconstruction/sinogram_cuda.py +1 -0
- nabu/reconstruction/sinogram_opencl.py +3 -1
- nabu/reconstruction/tests/test_cone.py +10 -5
- nabu/reconstruction/tests/test_deringer.py +7 -6
- nabu/reconstruction/tests/test_fbp.py +124 -10
- nabu/reconstruction/tests/test_filtering.py +13 -11
- nabu/reconstruction/tests/test_halftomo.py +30 -4
- nabu/reconstruction/tests/test_mlem.py +91 -0
- nabu/reconstruction/tests/test_reconstructor.py +8 -3
- nabu/resources/dataset_analyzer.py +142 -92
- nabu/resources/gpu.py +1 -0
- nabu/resources/nxflatfield.py +134 -125
- nabu/resources/templates/id16a_fluo.conf +42 -0
- nabu/resources/tests/test_extract.py +10 -0
- nabu/resources/tests/test_nxflatfield.py +2 -2
- nabu/stitching/alignment.py +80 -24
- nabu/stitching/config.py +105 -68
- nabu/stitching/definitions.py +1 -0
- nabu/stitching/frame_composition.py +68 -60
- nabu/stitching/overlap.py +91 -51
- nabu/stitching/single_axis_stitching.py +32 -0
- nabu/stitching/slurm_utils.py +6 -6
- nabu/stitching/stitcher/__init__.py +0 -0
- nabu/stitching/stitcher/base.py +124 -0
- nabu/stitching/stitcher/dumper/__init__.py +3 -0
- nabu/stitching/stitcher/dumper/base.py +94 -0
- nabu/stitching/stitcher/dumper/postprocessing.py +356 -0
- nabu/stitching/stitcher/dumper/preprocessing.py +60 -0
- nabu/stitching/stitcher/post_processing.py +555 -0
- nabu/stitching/stitcher/pre_processing.py +1068 -0
- nabu/stitching/stitcher/single_axis.py +484 -0
- nabu/stitching/stitcher/stitcher.py +0 -0
- nabu/stitching/stitcher/y_stitcher.py +13 -0
- nabu/stitching/stitcher/z_stitcher.py +45 -0
- nabu/stitching/stitcher_2D.py +278 -0
- nabu/stitching/tests/test_config.py +12 -37
- nabu/stitching/tests/test_frame_composition.py +33 -59
- nabu/stitching/tests/test_overlap.py +149 -7
- nabu/stitching/tests/test_utils.py +1 -1
- nabu/stitching/tests/test_y_preprocessing_stitching.py +132 -0
- nabu/stitching/tests/{test_z_stitching.py → test_z_postprocessing_stitching.py} +167 -561
- nabu/stitching/tests/test_z_preprocessing_stitching.py +431 -0
- nabu/stitching/utils/__init__.py +1 -0
- nabu/stitching/utils/post_processing.py +281 -0
- nabu/stitching/utils/tests/test_post-processing.py +21 -0
- nabu/stitching/{utils.py → utils/utils.py} +79 -52
- nabu/stitching/y_stitching.py +27 -0
- nabu/stitching/z_stitching.py +32 -2263
- nabu/testutils.py +1 -152
- nabu/thirdparty/tomocupy_remove_stripe.py +43 -9
- nabu/utils.py +158 -61
- {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/METADATA +10 -3
- {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/RECORD +144 -121
- nabu/io/tiffwriter_zmm.py +0 -99
- nabu/pipeline/fallback_utils.py +0 -149
- nabu/pipeline/helical/tests/test_accumulator.py +0 -158
- nabu/pipeline/helical/tests/test_pipeline_elements_full.py +0 -355
- nabu/pipeline/helical/tests/test_strategy.py +0 -61
- nabu/pipeline/helical/utils.py +0 -51
- nabu/pipeline/tests/test_chunk_reader.py +0 -74
- {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/LICENSE +0 -0
- {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/WHEEL +0 -0
- {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/entry_points.txt +0 -0
- {nabu-2024.1.9.dist-info → nabu-2024.2.0.dist-info}/top_level.txt +0 -0
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nabu/stitching/tests/test_overlap.py,sha256=B_iT0pe9b9EJ77V59ilk-_Run6n5a1V9mTDuiPzqieg,7820
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nabu/stitching/tests/test_slurm_utils.py,sha256=bbhCQd06R3irGB4B9r79KKlf0AlBchI53N2ldsXoAQQ,4950
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nabu/stitching/tests/test_z_postprocessing_stitching.py,sha256=kKRb3PvMOnCW84S58eQXSGcBpC7MiCZ6CXv_WDw0fP0,26915
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nabu/stitching/tests/test_z_preprocessing_stitching.py,sha256=3EhX161S2JVz6z3vXnYgBlUUQVb1weXBqIR0KAXLeUg,16157
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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=EssaIs7eUL1vrImJIi_Y5OzHHdEaoVedHAGWcOT8M6k,24650
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nabu/stitching/utils/tests/test_post-processing.py,sha256=Xy0UW8sL7ERtrxN7lEZhm8gJukDeL8vxkliMT8Agvas,753
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nabu/thirdparty/algotom_convert_sino.py,sha256=iZVRilvyqMyLTu8RKgbqDFUjObWW5X69rCARrnNizuI,13872
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nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtCl6G2NebJlbg,4500
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nabu/thirdparty/tomocupy_remove_stripe.py,sha256=
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nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
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nabu-2024.2.0.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
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nabu-2024.2.0.dist-info/METADATA,sha256=u-pY_1lM9XNtC-flH62tD52Vi6ZTMQFFZjICdc9YoyI,5538
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nabu-2024.2.0.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
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nabu-2024.2.0.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
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nabu-2024.2.0.dist-info/RECORD,,
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nabu/io/tiffwriter_zmm.py
DELETED
@@ -1,99 +0,0 @@
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from . import *
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from .writer import TIFFWriter as StandardTIFFWriter
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from os import path
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from tifffile import TiffWriter
|
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import numpy as np
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class TIFFWriter(StandardTIFFWriter): # pylint: disable=E0102
|
9
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def __init__(
|
10
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-
self,
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-
fname,
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multiframe=False,
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start_index=0,
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heights_above_stage_mm=None,
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filemode=None,
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append=False,
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big_tiff=None,
|
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-
):
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-
"""
|
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Tiff writer.
|
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-
|
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|
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Parameters
|
23
|
-
-----------
|
24
|
-
fname: str
|
25
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Path to the output file name
|
26
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multiframe: bool, optional
|
27
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Whether to write all data in one single file. Default is False.
|
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start_index: int, optional
|
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When writing a stack of images, each image is written in a dedicated file
|
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-
(unless multiframe is set to True).
|
31
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-
In this case, the output is a series of files `filename_0000.tif`,
|
32
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-
`filename_0001.tif`, etc. This parameter is the starting index for
|
33
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-
file names.
|
34
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This option is ignored when multiframe is True.
|
35
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heights_above_stage_mm: None or a list of heights
|
36
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-
if this parameters is given, the file names will be indexed with the height
|
37
|
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filemode: str, optional
|
38
|
-
DEPRECATED. Will be ignored. Please refer to 'append'
|
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-
append: bool, optional
|
40
|
-
Whether to append data to the file rather than overwriting. Default is False.
|
41
|
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big_tiff: bool, optional
|
42
|
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Whether to write in "big tiff" format: https://www.awaresystems.be/imaging/tiff/bigtiff.html
|
43
|
-
Default is True when multiframe is True.
|
44
|
-
Note that default "standard" tiff cannot exceed 4 GB.
|
45
|
-
|
46
|
-
Notes
|
47
|
-
------
|
48
|
-
If multiframe is False (default), then each image will be written in a
|
49
|
-
dedicated tiff file.
|
50
|
-
"""
|
51
|
-
super().__init__(
|
52
|
-
fname, multiframe=multiframe, start_index=start_index, filemode=filemode, append=append, big_tiff=big_tiff
|
53
|
-
)
|
54
|
-
self.heights_above_stage_mm = heights_above_stage_mm
|
55
|
-
|
56
|
-
def _write_tiff(self, data, config=None, filename=None):
|
57
|
-
# TODO metadata
|
58
|
-
filename = filename or self.fname
|
59
|
-
with TiffWriter(filename, bigtiff=self.big_tiff, append=self.append) as tif:
|
60
|
-
tif.write(data)
|
61
|
-
|
62
|
-
def write(self, data, *args, config=None, **kwargs):
|
63
|
-
# Single image, or multiple image in the same file
|
64
|
-
if self.multiframe:
|
65
|
-
self._write_tiff(data, config=config)
|
66
|
-
# Multiple image, one file per image
|
67
|
-
else:
|
68
|
-
if len(data.shape) == 2:
|
69
|
-
data = np.array([data])
|
70
|
-
dirname, rel_filename = path.split(self.fname)
|
71
|
-
prefix, ext = path.splitext(rel_filename)
|
72
|
-
for i in range(data.shape[0]):
|
73
|
-
if self.heights_above_stage_mm is None:
|
74
|
-
curr_rel_filename = prefix + str("_%06d" % (self.start_index + i)) + ext
|
75
|
-
else:
|
76
|
-
value_mm = self.heights_above_stage_mm[i]
|
77
|
-
if value_mm < 0:
|
78
|
-
sign = "-"
|
79
|
-
value_mm = -value_mm
|
80
|
-
else:
|
81
|
-
sign = ""
|
82
|
-
|
83
|
-
part_mm = int(value_mm)
|
84
|
-
rest_um = (value_mm - part_mm) * 1000
|
85
|
-
part_um = int(rest_um)
|
86
|
-
rest_nm = (rest_um - part_um) * 10
|
87
|
-
part_nm = int(rest_nm)
|
88
|
-
|
89
|
-
curr_rel_filename = prefix + "_{}{:04d}p{:03d}{:1d}".format(sign, part_mm, part_um, part_nm) + ext
|
90
|
-
|
91
|
-
fname = path.join(dirname, curr_rel_filename)
|
92
|
-
|
93
|
-
self._write_tiff(data[i], filename=fname, config=None)
|
94
|
-
|
95
|
-
def get_filename(self):
|
96
|
-
if self.multiframe:
|
97
|
-
return self.fname
|
98
|
-
else:
|
99
|
-
return path.dirname(self.fname)
|