tomwer 1.4.17__tar.gz → 1.4.18__tar.gz

{tomwer-1.4.17 → tomwer-1.4.18}/PKG-INFO

@@ -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 → tomwer-1.4.18}/setup.cfg

@@ -35,7 +35,7 @@ install_requires =
 	psutil
 	silx[full] >= 2.0,<2.1.1
 	tomoscan>=2.1.0a18
-	nxtomo>=1.3.0dev4
+	nxtomo>=1.3.0dev4,<2.0
 	nxtomomill>=1.1.0a0
 	processview>=1.5.0
 	ewoks>=0.1.1
@@ -108,7 +108,7 @@ full_base =
 	json-rpc
 	scipy
 	Pillow
-	glymur
+	glymur<0.14  # for python3.9 until https://github.com/quintusdias/glymur/issues/688 is fixed
 	resource
 	tifffile
 	hdf5plugin

{tomwer-1.4.17 → tomwer-1.4.18}/src/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-1.4.17 → tomwer-1.4.18}/src/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-1.4.17 → tomwer-1.4.18}/src/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-1.4.17 → tomwer-1.4.18}/src/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 → tomwer-1.4.18}/src/tomwer.egg-info/PKG-INFO

@@ -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 → tomwer-1.4.18}/src/tomwer.egg-info/SOURCES.txt

@@ -428,7 +428,6 @@ src/tomwer/core/scan/tests/__init__.py
 src/tomwer/core/scan/tests/test_edf.py
 src/tomwer/core/scan/tests/test_future_scan.py
 src/tomwer/core/scan/tests/test_nxtomoscan.py
-src/tomwer/core/scan/tests/test_process_registration.py
 src/tomwer/core/scan/tests/test_scan.py
 src/tomwer/core/tests/__init__.py
 src/tomwer/core/tests/test_scanutils.py
@@ -861,7 +860,6 @@ src/tomwer/synctools/tests/test_darkRefs.py
 src/tomwer/synctools/tests/test_foldertransfer.py
 src/tomwer/synctools/utils/__init__.py
 src/tomwer/synctools/utils/scanstages.py
-src/tomwer/tasks/reconstruction/cleardarkflat.py
 src/tomwer/tests/__init__.py
 src/tomwer/tests/conftest.py
 src/tomwer/tests/datasets.py

{tomwer-1.4.17 → tomwer-1.4.18}/src/tomwer.egg-info/requires.txt

@@ -3,7 +3,7 @@ setuptools
 psutil
 silx[full]<2.1.1,>=2.0
 tomoscan>=2.1.0a18
-nxtomo>=1.3.0dev4
+nxtomo<2.0,>=1.3.0dev4
 nxtomomill>=1.1.0a0
 processview>=1.5.0
 ewoks>=0.1.1
@@ -26,7 +26,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -53,7 +53,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -84,7 +84,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -113,7 +113,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -136,7 +136,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -156,7 +156,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -177,7 +177,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin
@@ -201,7 +201,7 @@ werkzeug
 json-rpc
 scipy
 Pillow
-glymur
+glymur<0.14
 resource
 tifffile
 hdf5plugin

tomwer-1.4.17/src/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-1.4.17/src/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