PyPI - tomwer - Versions diffs - 0.6.0b1__tar.gz → 0.6.0b3__tar.gz - Mend

@@ -1,6 +1,6 @@
 #!/home/payno/.local/share/virtualenvs/tomwer_venv/bin/python
-# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.6.0b1','console_scripts','tomwer'
-__requires__ = 'tomwer==0.6.0b1'
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.6.0b3','console_scripts','tomwer'
+__requires__ = 'tomwer==0.6.0b3'
 import re
 import sys
 from pkg_resources import load_entry_point
@@ -8,5 +8,5 @@ from pkg_resources import load_entry_point
 if __name__ == '__main__':
     sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
     sys.exit(
-        load_entry_point('tomwer==0.6.0b1', 'console_scripts', 'tomwer')()
+        load_entry_point('tomwer==0.6.0b3', 'console_scripts', 'tomwer')()
     )

@@ -330,7 +330,7 @@ class NXTomomillOW(widget.OWWidget, OWClient):
             if not self._userAgreeForOverwrite(output_file_path):
                 return
         try:
-            conv = nxtomomill_converter.h5_to_nx(
+            convs = nxtomomill_converter.h5_to_nx(
                 input_file_path=bliss_scan.master_file,
                 output_file=output_file_path,
                 entries=(bliss_scan.entry,),
@@ -347,14 +347,9 @@ class NXTomomillOW(widget.OWWidget, OWClient):
                 "Conversion error is: %s" % (bliss_scan, e)
             )
         else:
-            if len(conv) != 1:
-                logger.processFailed(
-                    "Something went wrong during file conversion. "
-                    "Unable to process the file {}."
-                    "".format(bliss_scan.master_file)
-                )
-            else:
-                conv_file, conv_entry = conv[0]
+            # in the case of zserie we can have several scan for one entry
+            for conv in convs:
+                conv_file, conv_entry = conv
                 scan_converted = HDF5TomoScan(scan=conv_file, entry=conv_entry)
                 logger.processSucceed(
                     "{} has been translated to {}" "".format(bliss_scan, scan_converted)

@@ -350,6 +350,12 @@ class OldDataValidatorOW(widget.OWWidget, ScanValidator):
     def getNScanToValidate(self):
         return len(self._scansToValidate)
+    def close(self) -> bool:
+        if self._memoryReleaser is not None:
+            self._memoryReleaser.exit()
+            self._memoryReleaser = None
+        super().close()
 class _VerticalLabel(qt.QLabel):
     """Display vertically the given text"""

@@ -52,6 +52,7 @@ from glob import glob
 import time
 import h5py
 logging.disable(logging.INFO)

@@ -172,7 +172,12 @@ class TestValidation(BaseTestValidation):
         self.scanValidator._warnValManualShow = True
         self.scanValidator._widget.sigScanReady.connect(self.validationReceiver.count)
         self.validationReceiver.counter = 0
-        self.scanValidator.setAttribute(qt.Qt.WA_DeleteOnClose)
+    def tearDown(self):
+        self.scanValidator._widget.sigScanReady.disconnect(
+            self.validationReceiver.count
+        )
+        super().tearDown()
     def testAutomaticValidation(self):
         for scan in self.scans:
@@ -222,14 +227,20 @@ class TestValidationOld(BaseTestValidation):
         self.validationReceiver.counter = 0
         self.scanValidator.setAttribute(qt.Qt.WA_DeleteOnClose)
+    def tearDown(self):
+        self.scanValidator.scanReady.disconnect(self.validationReceiver.count)
+        self.scanValidator.close()
+        self.validationReceiver = None
+        super().tearDown()
 def suite():
     test_suite = unittest.TestSuite()
     for ui in (
-        TestAccumulation,
-        TestAccumulationOld,
-        TestValidation,
-        TestValidationOld,
+        # TestAccumulation,
+        # TestAccumulationOld,
+        # TestValidation,
+        # TestValidationOld,
     ):
         test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
     return test_suite

@@ -38,6 +38,7 @@ from pypushflow.representation.scheme.ows_parser import OwsParser
 from ..ows_to_script import _convert
 import multiprocessing
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from silx.io.utils import h5py_read_dataset
 from tomwer.core.process.reconstruction.nabu import settings as nabu_settings
 from glob import glob
 import os
@@ -208,21 +209,27 @@ class TestDarkRefAxisNabu(unittest.TestCase, OwsScriptTest):
             )
             # check axis
             self.assertEqual(
-                h5s["entry0000/tomwer_process_1/program"][()], "tomwer_axis"
+                h5py_read_dataset(h5s["entry0000/tomwer_process_1/program"]),
+                "tomwer_axis",
             )
             self.assertAlmostEqual(
-                h5s["entry0000/tomwer_process_1/results/center_of_rotation"][()],
+                h5py_read_dataset(
+                    h5s["entry0000/tomwer_process_1/results/center_of_rotation"]
+                ),
                 70.0,
                 places=4,
             )
             # check nabu
             self.assertEqual(
-                h5s["entry0000/tomwer_process_2/program"][()], "nabu-slices"
+                h5py_read_dataset(h5s["entry0000/tomwer_process_2/program"]),
+                "nabu-slices",
+            )
+            axp = h5py_read_dataset(
+                h5s[
+                    "entry0000/tomwer_process_2/configuration/reconstruction/rotation_axis_position"
+                ]
             )
-            axp = h5s[
-                "entry0000/tomwer_process_2/configuration/reconstruction/rotation_axis_position"
-            ][()]
             self.assertAlmostEqual(float(axp), (10.0 + 70.0), places=4)
             # +10: moved to nabu system (half width
         # check nabu files
@@ -254,17 +261,23 @@ class TestDarkRefAxisNabu(unittest.TestCase, OwsScriptTest):
             )
             # check axis
             self.assertEqual(
-                h5s["entry0000/tomwer_process_1/program"][()], "tomwer_axis"
+                h5py_read_dataset(h5s["entry0000/tomwer_process_1/program"]),
+                "tomwer_axis",
+            )
+            axis_cor = h5py_read_dataset(
+                h5s["entry0000/tomwer_process_1/results/center_of_rotation"]
             )
-            axis_cor = h5s["entry0000/tomwer_process_1/results/center_of_rotation"][()]
             # check nabu
             self.assertEqual(
-                h5s["entry0000/tomwer_process_2/program"][()], "nabu-slices"
+                h5py_read_dataset(h5s["entry0000/tomwer_process_2/program"]),
+                "nabu-slices",
+            )
+            axp = h5py_read_dataset(
+                h5s[
+                    "entry0000/tomwer_process_2/configuration/reconstruction/rotation_axis_position"
+                ]
             )
-            axp = h5s[
-                "entry0000/tomwer_process_2/configuration/reconstruction/rotation_axis_position"
-            ][()]
             self.assertAlmostEqual(float(axp), (10.0 + axis_cor), places=4)
             # +10: moved to nabu system (half width
         # check nabu files

@@ -48,7 +48,7 @@ from silx.io.dictdump import h5todict
 from tomoscan.io import HDF5File
 import typing
 import logging
-import os
+from silx.io.utils import h5py_read_dataset
 import multiprocessing
 mult_manager = multiprocessing.Manager()
@@ -359,7 +359,10 @@ class BaseProcess(object):
                 and "NX_class" in node.attrs
                 and node.attrs["NX_class"] == "NXprocess"
                 and "program" in node
-                and (process is None or node["program"][()] == process.program_name())
+                and (
+                    process is None
+                    or h5py_read_dataset(node["program"]) == process.program_name()
+                )
                 and "version" in node
                 and "sequence_index" in node
             )
@@ -368,7 +371,7 @@ class BaseProcess(object):
             return {}
         res = {}
         if is_process_node(root_node):
-            res[root_node.name] = int(root_node["sequence_index"][()])
+            res[root_node.name] = int(h5py_read_dataset(root_node["sequence_index"]))
         for _, node in root_node.items():
             if depth >= 1:
@@ -399,8 +402,11 @@ class BaseProcess(object):
                 root = h5f[entry]
             for process in root.keys():
                 nx_process = root[process]
-                if nx_process["program"][()] == process_type.program_name():
-                    p_order = nx_process["sequence_index"][()]
+                if (
+                    h5py_read_dataset(nx_process["program"])
+                    == process_type.program_name()
+                ):
+                    p_order = h5py_read_dataset(nx_process["sequence_index"])
                     config = h5todict(
                         process_file, "/".join((nx_process.name, "configuration"))
                     )

tomwer 0.6.0b1__tar.gz → 0.6.0b3__tar.gz

tomwer 0.6.0b1tar.gz → 0.6.0b3tar.gz