tomwer 1.4.17__py3-none-any.whl → 1.4.18__py3-none-any.whl

tomwer/app/nabuapp.py

@@ -95,7 +95,9 @@ class NabuWindow(NabuDialog):
 
         # add center of rotation widget
         self._corWidget = _CORWidget(parent=self)
-        rw = self._widget._mainWidget._configuration._reconstructionWidget
+        rw = (
+            self._widget._mainWidget._nabuSettingsWidget._configuration._reconstructionWidget
+        )
         rw.layout().addWidget(self._corWidget, 99, 0, 1, 2)
 
         self._dataViewer = None

tomwer/core/scan/nxtomoscan.py

@@ -427,7 +427,7 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
             )
         return {
             "hdf5_entry": self.entry,
-            "location": os.path.basename(self.master_file),
+            "location": filter_esrf_mounting_points(os.path.abspath(self.master_file)),
             "binning": binning,
             "binning_z": binning_z,
             "projections_subsampling": proj_subsampling,

tomwer/gui/utils/utils.py

@@ -49,7 +49,7 @@ def open_url_with_image_j(url: DataUrl) -> threading.Thread:
 
     :param url: url we want to open in imagej
     """
-    global __image_j_from
+    global __image_j_from  # noqa: F824
     if not has_imagej():
         raise OSError("ImageJ is not installed")
     thread = ImageJthread(url=url, image_j_from=__image_j_from)

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 4
-MICRO = 17
+MICRO = 18
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.4.17.dist-info → tomwer-1.4.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 1.4.17
+Version: 1.4.18
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -26,7 +26,7 @@ Requires-Dist: setuptools
 Requires-Dist: psutil
 Requires-Dist: silx[full]<2.1.1,>=2.0
 Requires-Dist: tomoscan>=2.1.0a18
-Requires-Dist: nxtomo>=1.3.0dev4
+Requires-Dist: nxtomo<2.0,>=1.3.0dev4
 Requires-Dist: nxtomomill>=1.1.0a0
 Requires-Dist: processview>=1.5.0
 Requires-Dist: ewoks>=0.1.1
@@ -48,7 +48,7 @@ Requires-Dist: werkzeug; extra == "full-base"
 Requires-Dist: json-rpc; extra == "full-base"
 Requires-Dist: scipy; extra == "full-base"
 Requires-Dist: Pillow; extra == "full-base"
-Requires-Dist: glymur; extra == "full-base"
+Requires-Dist: glymur<0.14; extra == "full-base"
 Requires-Dist: resource; extra == "full-base"
 Requires-Dist: tifffile; extra == "full-base"
 Requires-Dist: hdf5plugin; extra == "full-base"
@@ -68,7 +68,7 @@ Requires-Dist: werkzeug; extra == "full-no-nabu"
 Requires-Dist: json-rpc; extra == "full-no-nabu"
 Requires-Dist: scipy; extra == "full-no-nabu"
 Requires-Dist: Pillow; extra == "full-no-nabu"
-Requires-Dist: glymur; extra == "full-no-nabu"
+Requires-Dist: glymur<0.14; extra == "full-no-nabu"
 Requires-Dist: resource; extra == "full-no-nabu"
 Requires-Dist: tifffile; extra == "full-no-nabu"
 Requires-Dist: hdf5plugin; extra == "full-no-nabu"
@@ -88,7 +88,7 @@ Requires-Dist: werkzeug; extra == "full-no-cuda"
 Requires-Dist: json-rpc; extra == "full-no-cuda"
 Requires-Dist: scipy; extra == "full-no-cuda"
 Requires-Dist: Pillow; extra == "full-no-cuda"
-Requires-Dist: glymur; extra == "full-no-cuda"
+Requires-Dist: glymur<0.14; extra == "full-no-cuda"
 Requires-Dist: resource; extra == "full-no-cuda"
 Requires-Dist: tifffile; extra == "full-no-cuda"
 Requires-Dist: hdf5plugin; extra == "full-no-cuda"
@@ -109,7 +109,7 @@ Requires-Dist: werkzeug; extra == "full"
 Requires-Dist: json-rpc; extra == "full"
 Requires-Dist: scipy; extra == "full"
 Requires-Dist: Pillow; extra == "full"
-Requires-Dist: glymur; extra == "full"
+Requires-Dist: glymur<0.14; extra == "full"
 Requires-Dist: resource; extra == "full"
 Requires-Dist: tifffile; extra == "full"
 Requires-Dist: hdf5plugin; extra == "full"
@@ -132,7 +132,7 @@ Requires-Dist: werkzeug; extra == "doc"
 Requires-Dist: json-rpc; extra == "doc"
 Requires-Dist: scipy; extra == "doc"
 Requires-Dist: Pillow; extra == "doc"
-Requires-Dist: glymur; extra == "doc"
+Requires-Dist: glymur<0.14; extra == "doc"
 Requires-Dist: resource; extra == "doc"
 Requires-Dist: tifffile; extra == "doc"
 Requires-Dist: hdf5plugin; extra == "doc"
@@ -166,7 +166,7 @@ Requires-Dist: werkzeug; extra == "dev"
 Requires-Dist: json-rpc; extra == "dev"
 Requires-Dist: scipy; extra == "dev"
 Requires-Dist: Pillow; extra == "dev"
-Requires-Dist: glymur; extra == "dev"
+Requires-Dist: glymur<0.14; extra == "dev"
 Requires-Dist: resource; extra == "dev"
 Requires-Dist: tifffile; extra == "dev"
 Requires-Dist: hdf5plugin; extra == "dev"
@@ -193,7 +193,7 @@ Requires-Dist: werkzeug; extra == "dev-no-cuda"
 Requires-Dist: json-rpc; extra == "dev-no-cuda"
 Requires-Dist: scipy; extra == "dev-no-cuda"
 Requires-Dist: Pillow; extra == "dev-no-cuda"
-Requires-Dist: glymur; extra == "dev-no-cuda"
+Requires-Dist: glymur<0.14; extra == "dev-no-cuda"
 Requires-Dist: resource; extra == "dev-no-cuda"
 Requires-Dist: tifffile; extra == "dev-no-cuda"
 Requires-Dist: hdf5plugin; extra == "dev-no-cuda"
@@ -218,7 +218,7 @@ Requires-Dist: werkzeug; extra == "test"
 Requires-Dist: json-rpc; extra == "test"
 Requires-Dist: scipy; extra == "test"
 Requires-Dist: Pillow; extra == "test"
-Requires-Dist: glymur; extra == "test"
+Requires-Dist: glymur<0.14; extra == "test"
 Requires-Dist: resource; extra == "test"
 Requires-Dist: tifffile; extra == "test"
 Requires-Dist: hdf5plugin; extra == "test"

{tomwer-1.4.17.dist-info → tomwer-1.4.18.dist-info}/RECORD

@@ -219,7 +219,7 @@ orangecontrib/tomwer/widgets/visualization/tests/__init__.py,sha256=47DEQpj8HBSa
 tomwer/__init__.py,sha256=cMIyH-uRxpa9WVnAuWjiBD7k9TK57WO21RzP_S-Mb8I,460
 tomwer/__main__.py,sha256=7tCADiS4u7k1PCxFhlRAcYSIOpxQTGUTx8sCEQ-hi1E,8707
 tomwer/utils.py,sha256=7h7dEgKAEUmQ43jkULvC1B9Adl55nkCty-SEKUKCl4U,7008
-tomwer/version.py,sha256=bLV36WJKGROMwVXzqAZ8PSBx-f4ml945UwWkG4kKaug,4387
+tomwer/version.py,sha256=ZockRUONTpS2pMmqMM74e8Rvh1TysPALNWyegIXFEyE,4387
 tomwer/app/__init__.py,sha256=h1FKED7Tw5f99yikygt7ruXsdrxQhcJxO7kagLGxhJg,84
 tomwer/app/axis.py,sha256=lB-IZx1o6KTWLIelITvYCIu2flFTB9NhuIfD2MhUZZA,5826
 tomwer/app/canvas.py,sha256=y8rYOiwmv6ug7JcjgkOzEiGQnNXjKWNNmKofT0n8TFg,1538
@@ -231,7 +231,7 @@ tomwer/app/imagekeyupgrader.py,sha256=qLbfWPz68b2DxMYNd5MlIyZdQ12YQ7F-KUA92RcI01
 tomwer/app/intensitynormalization.py,sha256=5uT8xQWjjq7uV8-0jru_2Qf9SIN5ooVCPH8Ok8inMYE,5998
 tomwer/app/multicor.py,sha256=NgSYIh1CTM1ssD5fXfH4j9MM3HU_NUEx_4EIWehijMs,8900
 tomwer/app/multipag.py,sha256=LHk4-97aYqFQ9UgQb8mYW1_nkUQBbgUxee4RinloCjk,12016
-tomwer/app/nabuapp.py,sha256=f8mao2GprCN-CCTFHUlrCLoxFNZmMpzegrlMNnyE_XI,7643
+tomwer/app/nabuapp.py,sha256=1kBQlyzkEYW-iEH6hdYlrXuvg1MPQfPLmDIA5P6oXE4,7687
 tomwer/app/nxtomoeditor.py,sha256=1Wj59ZF3QvDBmUkUosxZlxvOM-mCvs74l1YJe3tFtwQ,3012
 tomwer/app/patchrawdarkflat.py,sha256=0s4Uk7rlF6VYcwKAysxj5ncP7jTgDL9XIiMPqZUktvg,3779
 tomwer/app/radiostack.py,sha256=S6VB7BSmpfFdnGEyX_7wvLFiOtbtlEwgP7PEUAJLN4w,2640
@@ -408,7 +408,7 @@ tomwer/core/scan/edfscan.py,sha256=5brP6ewiDRaT0ssSf35kAYzfWwynyTaoSPcOjmNxf0o,2
 tomwer/core/scan/futurescan.py,sha256=chXjteQ4_6cSyFBoCil-DeHkHGGzM-xb21xJRYLEfhI,213
 tomwer/core/scan/hdf5scan.py,sha256=rQ-WtbOIgNtnMxA2kC23fEAcJIJIKboAv7UQColkrBg,966
 tomwer/core/scan/helicalmetadata.py,sha256=JRBxqHkyTe5f3FDlbIeDfN31P6Ms48SqGiFRXHuZ8sw,472
-tomwer/core/scan/nxtomoscan.py,sha256=wfyTtgxSaazxacUyUxdESJldUTbpJ8G-NhF09xO1XGI,18413
+tomwer/core/scan/nxtomoscan.py,sha256=juA5so5YpiLDC4-JMCcR5xNovCRbLmcEkWN65QfWkzk,18441
 tomwer/core/scan/scanbase.py,sha256=GO5DgYHtLZJwLW1-Y4ztHxgfdGMPUIhx1rhBG9lWBeM,25627
 tomwer/core/scan/scanfactory.py,sha256=-bF0Ru9bn8bnGk4MKXhbt5Oli19qN1WvFPDMtqw81BA,9116
 tomwer/core/scan/scantype.py,sha256=pQjWuCy_014uK5cdb8pFAkE_EPHJvPdSo3NM8aWTo58,137
@@ -416,7 +416,6 @@ tomwer/core/scan/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 tomwer/core/scan/tests/test_edf.py,sha256=JI7wH5emdjlYl08OhmjIO_8mui7rHa-aRCUwmkCRyys,830
 tomwer/core/scan/tests/test_future_scan.py,sha256=tsF9p57dCOmW0fPyl6BP2lLSo0rRYRF6hSF-kryLMDM,848
 tomwer/core/scan/tests/test_nxtomoscan.py,sha256=w2mNuCsfWMl1b9jP_-vkTDkCD_z9oM02yx42f6-DzY8,4751
-tomwer/core/scan/tests/test_process_registration.py,sha256=g4Toef92SjxCBUE82MTbjonFJpc3PQqfpF6FSCarN5U,1988
 tomwer/core/scan/tests/test_scan.py,sha256=mHFPi2Tc7Z2_5rWvAp3YmObVSTB5yi-sTkHm1iOJlDo,12228
 tomwer/core/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/tests/test_scanutils.py,sha256=xWwd1nycVDWmFaIaL2gQ_xxrUMhVCARaNHI2SxT9NOI,844
@@ -651,7 +650,7 @@ tomwer/gui/utils/slider.py,sha256=NLooxIa_2dMv60UAt_PV2BKcd15WuNv1EiV1JRdVcu0,21
 tomwer/gui/utils/splashscreen.py,sha256=Wt6lDby3irZn6Vc52whPRTbJOzmMA66VH6d5cIXy_dI,489
 tomwer/gui/utils/step.py,sha256=epEKQwj2byRFH_Lc2XUuMGOVcrKR0m1iFP7HPqb5iG0,5397
 tomwer/gui/utils/unitsystem.py,sha256=0g6pYemy2MpkGQJGuuR9yCwbZ9mt3nPA1dqAvAqUHRo,5994
-tomwer/gui/utils/utils.py,sha256=e_PA4P8GjBW17uemqSDjMy5YLYgVIy2qppmP2kYTALU,2673
+tomwer/gui/utils/utils.py,sha256=FbzvEkJacSdZXe4lvrYOge9csQGx50hH-R8gbx5E0sI,2687
 tomwer/gui/utils/vignettes.py,sha256=1HoABQcreptH6GIuo5nrLZmPcsTWuQlRuSW5IHJTRT4,17792
 tomwer/gui/utils/waiterthread.py,sha256=lyRCzVDAyxquO3JbXxDhVTCv_YjzOQd7PAPsGWjKBrE,494
 tomwer/gui/utils/lineselector/__init__.py,sha256=GZ847ef5X2wk_sAHxg6h24TarPYmb4NZjQI3jjkc7jE,75
@@ -849,7 +848,6 @@ tomwer/synctools/tests/test_darkRefs.py,sha256=1OgWaV-hgDmi4rkh0hxjCW_codBAnxNhp
 tomwer/synctools/tests/test_foldertransfer.py,sha256=ZFIJWSjgYAWw3ktzamid5DJZNnMkAV6Pj72dKG69cJc,12024
 tomwer/synctools/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/synctools/utils/scanstages.py,sha256=vIUKVDSfM2UwPjjmZTiIN1tNg4antnGcSPv1aYapJCY,7830
-tomwer/tasks/reconstruction/cleardarkflat.py,sha256=_V_x7W8vp1_AqqtQ9xk2VRgwlivn4IPTLEpWySjSZRE,1353
 tomwer/tests/__init__.py,sha256=dPPaIvpzHssjwxsMzYJM_gxQ2e0cnRyQHXxi9ux6ZOY,19
 tomwer/tests/conftest.py,sha256=0XlKfOrVtPg8VmyQn4BoK_mzcliFUtacDGLlZ5wD_PM,1912
 tomwer/tests/datasets.py,sha256=QXQ3jSwgWzfq4CaELOSrk9kHg5GmrP7kGHsdOlNSEIE,336
@@ -906,9 +904,9 @@ tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewer
 tomwer/tests/test_ewoks/test_conversion.py,sha256=a8cEWbErXiFCAkaapi0jeEoRKYxcFQCoa-Jr_u77_OM,3656
 tomwer/tests/test_ewoks/test_single_node_execution.py,sha256=YBUHfiAnkciv_kjj7biC5fOs7c7ofNImM_azGMn4LZM,2813
 tomwer/tests/test_ewoks/test_workflows.py,sha256=Eq80eexf5NVL7SzvwctLOaUeuQ8V3vDiFiHgbJA4Yb8,4871
-tomwer-1.4.17.dist-info/licenses/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.4.17.dist-info/METADATA,sha256=XwIaehtXQw8A82CKM2JkllfIOo_lKcvLJ5HFrsSCPpA,13438
-tomwer-1.4.17.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-tomwer-1.4.17.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.4.17.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.4.17.dist-info/RECORD,,
+tomwer-1.4.18.dist-info/licenses/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
+tomwer-1.4.18.dist-info/METADATA,sha256=JzR1mNQUR3mOwD1uqJNJKCE62eAa0U5Vy67pb2qNc5o,13483
+tomwer-1.4.18.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
+tomwer-1.4.18.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
+tomwer-1.4.18.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
+tomwer-1.4.18.dist-info/RECORD,,

{tomwer-1.4.17.dist-info → tomwer-1.4.18.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (79.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tomwer/core/scan/tests/test_process_registration.py

@@ -1,64 +0,0 @@
-# coding: utf-8
-from __future__ import annotations
-
-import shutil
-import tempfile
-import unittest
-
-from tomoscan.io import HDF5File, get_swmr_mode
-
-from tomwer.core.process.task import Task
-from tomwer.core.utils.scanutils import MockNXtomo
-
-
-class TestProcessRegistration(unittest.TestCase):
-    """
-    Make sure utils link to the process registration are
-    correctly working
-    """
-
-    class DummyProcess(Task):
-        @staticmethod
-        def program_name():
-            """Name of the program used for this processing"""
-            return "dummy program"
-
-        @staticmethod
-        def program_version():
-            """version of the program used for this processing"""
-            return "0.0.0"
-
-        @staticmethod
-        def definition():
-            """definition of the process"""
-            return "no definition"
-
-    def setUp(self):
-        self.tmp_dir = tempfile.mkdtemp()
-        self.scan = MockNXtomo(scan_path=self.tmp_dir, n_proj=2).scan
-
-    def tearDown(self):
-        shutil.rmtree(self.tmp_dir)
-
-    def testGetProcessNodes(self):
-        """insure it return the last dark process based on the processing index"""
-
-        for i in range(20):
-            Task._register_process(
-                self.scan.process_file,
-                process=self.DummyProcess,
-                entry=self.scan.entry,
-                configuration=None,
-                results={"output": i},
-                process_index=i,
-            )
-
-        with HDF5File(self.scan.process_file, "r", swmr=get_swmr_mode()) as h5f:
-            nodes = Task._get_process_nodes(
-                root_node=h5f[self.scan.entry], process=self.DummyProcess
-            )
-            self.assertEqual(len(nodes), 20)
-            self.assertTrue("/entry/tomwer_process_16" in nodes)
-            self.assertEqual(nodes["/entry/tomwer_process_16"], 16)
-            self.assertTrue("/entry/tomwer_process_1" in nodes)
-            self.assertEqual(nodes["/entry/tomwer_process_1"], 1)

tomwer/tasks/reconstruction/cleardarkflat.py

@@ -1,42 +0,0 @@
-"""
-Contains task to clear reduced dark and flat frames
-"""
-
-from __future__ import annotations
-
-from tomoscan.scanbase import TomoScanBase as TomoscanScanBase
-
-from processview.core.manager import DatasetState, ProcessManager
-from processview.core.superviseprocess import SuperviseProcess
-
-from tomwer.tasks.task import Task
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.utils.scanutils import data_identifier_to_scan
-from tomwer.core.reconstruction.darkflat import params as dkrf_reconsparams
-from tomwer.utils import docstring
-
-
-class ClearReducedDarkAndFlat(
-    Task,
-    SuperviseProcess,
-    input_names=("data",),
-    output_names=("data",),
-):
-    """
-    Task to clear reduced darks and flats. Both on disk and on the object cache.
-    th goal of this task is to make sure the scan is cleared of any reduced frames to reprocess it later.
-    """
-
-    def run(self):
-        scan = self.inputs.data
-        if not isinstance(scan, TomoscanScanBase):
-            raise TypeError(
-                f"scan should be an instance of {TomoscanScanBase}. Got {type(scan)}"
-            )
-        scan.set_reduced_flats(None)
-        scan.reduced_flats_infos = None
-        scan.set_reduced_darks(None)
-        scan.reduced_darks_infos = None
-
-        self.outputs.data = scan