nabu 2024.2.5__py3-none-any.whl → 2024.2.7__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.5"
+__version__ = "2024.2.7"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/pipeline/fullfield/reconstruction.py

@@ -131,8 +131,12 @@ class FullFieldReconstructor:
         self.resources["gpus"] = avail_gpus
         if len(avail_gpus) == 0:
             return
-        # pick first GPU by default. TODO: handle user's nabu_config["resources"]["gpu_id"]
-        self.resources["gpu_id"] = self._gpu_id = list(avail_gpus.keys())[0]
+        user_gpus = self.process_config.nabu_config.get("resources", {}).get("gpu_id", [])
+        if len(user_gpus) == 0:
+            user_gpus = [0]
+        # For now nabu does not support multi-GPU reconstruction. Take the first one.
+        user_gpu_idx = user_gpus[0]
+        self.resources["gpu_id"] = self._gpu_id = list(avail_gpus.keys())[user_gpu_idx]
 
     def _get_backend(self, backend, cuda_options):
         self._pipeline_cls = ChunkedPipeline
@@ -145,6 +149,7 @@ class FullFieldReconstructor:
                 backend = "numpy"
             else:
                 self.gpu_mem = self.resources["gpus"][self._gpu_id]["memory_GB"] * self.gpu_mem_fraction
+                self.cuda_options = {"device_id": self._gpu_id}
         if backend == "cuda":
             if not (__has_pycuda__):
                 raise RuntimeError("pycuda not avilable")

nabu/resources/dataset_analyzer.py

@@ -2,8 +2,10 @@ import os
 import numpy as np
 from silx.io.url import DataUrl
 from silx.io import get_data
+from tomoscan import __version__ as __tomoscan_version__
 from tomoscan.esrf.scan.edfscan import EDFTomoScan
 from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from packaging.version import parse as parse_version
 
 from ..utils import check_supported, indices_to_slices
 from ..io.reader import EDFStackReader, NXDarksFlats, NXTomoReader
@@ -143,7 +145,10 @@ class DatasetAnalyzer:
         Return the sample-detector distance in meters.
         """
         if self._distance is None:
-            self._distance = abs(self.dataset_scanner.distance)
+            if parse_version(__tomoscan_version__) < parse_version("2.2"):
+                self._distance = abs(self.dataset_scanner.distance)
+            else:
+                self._distance = abs(self.dataset_scanner.sample_detector_distance)
         return self._distance
 
     @distance.setter

nabu/stitching/utils/utils.py

@@ -1,4 +1,4 @@
-from distutils.version import StrictVersion
+from packaging.version import parse as parse_version
 from typing import Optional, Union
 import logging
 import functools
@@ -523,7 +523,7 @@ def find_shift_with_itk(img1: numpy.ndarray, img2: numpy.ndarray) -> tuple:
         _logger.warning("itk is not installed. Please install it to find shift with it")
         return (0, 0)
 
-    if StrictVersion(itk.Version.GetITKVersion()) < StrictVersion("4.9.0"):
+    if parse_version(itk.Version.GetITKVersion()) < parse_version("4.9.0"):
         _logger.error("ITK 4.9.0 is required to find shift with it.")
         return (0, 0)
 

{nabu-2024.2.5.dist-info → nabu-2024.2.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nabu
-Version: 2024.2.5
+Version: 2024.2.7
 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>

{nabu-2024.2.5.dist-info → nabu-2024.2.7.dist-info}/RECORD

@@ -1,7 +1,7 @@
 doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=BhsllrJ2adOlOshSRwCN9w9DtOegccwzs8GPbrfvAUA,270
+nabu/__init__.py,sha256=jfYqwDZB9SZV1cW-GiBKmgxrQpKNF9PxVpFn-1m65Yg,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -143,7 +143,7 @@ nabu/pipeline/fullfield/computations.py,sha256=AEp3qvwyY-l8-GzjH1E6kmcmU6OgDp6sB
 nabu/pipeline/fullfield/dataset_validator.py,sha256=Iy6oOnXnBldDcg0ifm_zzrzMQ6YdkR_hkHFySZgxbno,2943
 nabu/pipeline/fullfield/nabu_config.py,sha256=rvHmCNHx2y-GKBidRWCAjJd0IynvolPTTmBqNoOSvEA,31877
 nabu/pipeline/fullfield/processconfig.py,sha256=2eE9W0KjsHq8aSCXlczsISpWM9SMjWL03fN1RqZWyxg,36815
-nabu/pipeline/fullfield/reconstruction.py,sha256=fMHKR8LnpQ2_asIO5bJB3pRixABrKLi53KzJuB83NZ4,37422
+nabu/pipeline/fullfield/reconstruction.py,sha256=LpIMyl8LLJoJLhayHXT3VyOwRpEL9tdjPhIegFUS388,37678
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/helical/dataset_validator.py,sha256=0YQc0hdYdpaXznFaKmlj9SIu7mNs0xXMejcRkhOZHaI,640
 nabu/pipeline/helical/fbp.py,sha256=0fAz-Fb0Rn_FzellvcS2cy-Wvm-5dxEf494YFt4pLws,5845
@@ -249,7 +249,7 @@ nabu/reconstruction/tests/test_reconstructor.py,sha256=3p2Wk_OqgZqkNOkhK_NJWlHkO
 nabu/reconstruction/tests/test_sino_normalization.py,sha256=fGv5Dlidxgm8ZC70Nk6oqVgpY2jzOW9NJaGlo44IJOo,3692
 nabu/resources/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/resources/cor.py,sha256=-mcrTbj3G7o4PP5E_gIRo2j6_-ADmMkkOc_0CyQv84c,170
-nabu/resources/dataset_analyzer.py,sha256=e3AqYR9ORW9Q03mGYCiC66nXld-X0LPnx9E8X3zFIGU,18568
+nabu/resources/dataset_analyzer.py,sha256=ld5BHt023nM3o9QlyZS5v3UpKiKyRdnYic9QZgNGjuI,18859
 nabu/resources/gpu.py,sha256=GgpMb5umRQAUsEDEAefb4wSA5qm4JSMhkWmCEpW3X9g,5702
 nabu/resources/logger.py,sha256=-lOzhN_sU4R3BIfC69aMj2O8S_ocsvXsmwkhWlcxVEc,3758
 nabu/resources/nxflatfield.py,sha256=FhPqiXe6ZKu5eGI6aVfyTgcHhZF9kQUNX0cOxDPD73k,9324
@@ -262,7 +262,6 @@ nabu/resources/templates/id16_holo.conf,sha256=sDd_rEJGZjOGVAsGub5sT2arfXDnc_sxy
 nabu/resources/templates/id16a_fluo.conf,sha256=Nz1etzO2fSwksi7CThWJ5T1kZEdyBe8rMO7puNJ93Hc,542
 nabu/resources/templates/id19_pag.conf,sha256=u4fFPEBprzOW9_5_ChkIgowQcYpLhjmA8Gwm5XgC4Jc,384
 nabu/resources/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/resources/tests/test_extract.py,sha256=msYWFP96LjpEntq1ucTWgKZMhUvZcLpJ-AQB3oGOh2E,206
 nabu/resources/tests/test_nxflatfield.py,sha256=XRGbYwqJv0NYAVQnAB224TwTZP_W2Bs3-yu0zQnDzEM,4179
 nabu/resources/tests/test_units.py,sha256=F2jFTck-1UwYET1MwTtX6ntzYUosfwOJkugSencGgz8,2155
 nabu/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -302,7 +301,7 @@ nabu/stitching/tests/test_z_postprocessing_stitching.py,sha256=kKRb3PvMOnCW84S58
 nabu/stitching/tests/test_z_preprocessing_stitching.py,sha256=3EhX161S2JVz6z3vXnYgBlUUQVb1weXBqIR0KAXLeUg,16157
 nabu/stitching/utils/__init__.py,sha256=alIDGBnxWH4JvP-UW-7N99seBBi0r1GV1h8f1ERFBec,21
 nabu/stitching/utils/post_processing.py,sha256=aow36shbYhFgAnbCoq6mtXVpjBNCKm7VSLIvv3EYVdA,11303
-nabu/stitching/utils/utils.py,sha256=EssaIs7eUL1vrImJIi_Y5OzHHdEaoVedHAGWcOT8M6k,24650
+nabu/stitching/utils/utils.py,sha256=Z_JcVrUdykYFzeHJD8J-3y7kQb4Ef3_FM7M0zjQTPXg,24659
 nabu/stitching/utils/tests/test_post-processing.py,sha256=Xy0UW8sL7ERtrxN7lEZhm8gJukDeL8vxkliMT8Agvas,753
 nabu/thirdparty/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/thirdparty/algotom_convert_sino.py,sha256=iZVRilvyqMyLTu8RKgbqDFUjObWW5X69rCARrnNizuI,13872
@@ -310,9 +309,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=Khe4zFf0kRzu65Yxnvq58gt1ljOztqJGdMDhVAiM7lM,24363
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2024.2.5.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.5.dist-info/METADATA,sha256=dagapyWNaPkQX79F5M8U6pRfmPJqczjoupUC41I5yfw,5514
-nabu-2024.2.5.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nabu-2024.2.5.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.5.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.5.dist-info/RECORD,,
+nabu-2024.2.7.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.7.dist-info/METADATA,sha256=KhmcCqJFd0DXEKQ3YP42BSC5a7yedWK1Cx0VLsukF9s,5514
+nabu-2024.2.7.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nabu-2024.2.7.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.7.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.7.dist-info/RECORD,,

nabu/resources/tests/test_extract.py

@@ -1,9 +0,0 @@
-from nabu.utils import list_match_queries
-
-
-def test_list_match_queries():
-
-    # entry0000 .... entry0099
-    avail = ["entry%04d" % i for i in range(100)]
-    query = "entry0000"
-    list_match_queries()