tomwer 0.5.2b1__tar.gz → 0.5.2b2__tar.gz

users/payno/.local/share/virtualenvs/tomwer_venc/bin/tomwer

@@ -1,6 +1,6 @@
 #!/users/payno/.local/share/virtualenvs/tomwer_venc/bin/python
-# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.2b1','console_scripts','tomwer'
-__requires__ = 'tomwer==0.5.2b1'
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.2b2','console_scripts','tomwer'
+__requires__ = 'tomwer==0.5.2b2'
 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==0.5.2b1', 'console_scripts', 'tomwer')()
+        load_entry_point('tomwer==0.5.2b2', 'console_scripts', 'tomwer')()
     )

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/test/utils.py

@@ -312,7 +312,8 @@ class OrangeWorkflowMixIn:
         self.canvas_window.closeEvent = self.closeEventMonkeyPatch
         self.canvas_window.close()
         self.app.removePostedEvents(signal_manager)
-        del self.canvas_window
+        if hasattr(self, 'canvas_window'):
+            del self.canvas_window
         gc.collect()
         self.app.quit()
 

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/__init__.py

@@ -48,7 +48,7 @@ WIDGET_HELP_PATH = (
     # You still need to build help pages using
     # make htmlhelp
     # inside doc folder
-    ("{}/build/sphinx/htmlhelp/index.html", None),
+    ("/build/sphinx/htmlhelp/index.html", None),
     #
     # Documentation included in wheel
     # Correct DATA_FILES entry is needed in setup.py and documentation has to be built

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/DataListOW.py

@@ -82,7 +82,7 @@ class DataListOW(widget.OWWidget, OWClient):
         self.widget._sendButton.clicked.connect(self._sendList)
 
         # expose API
-        self.size = self.widget.size
+        self.n_scan = self.widget.n_scan
 
         # alias used for the 'simple workflow' for now
         self.start = self._sendList
@@ -98,19 +98,10 @@ class DataListOW(widget.OWWidget, OWClient):
             self.Outputs.data_out.send(scan_)
 
         for d in self.widget.datalist.items:
-            if '@' in d:
-                entry, scan_file_or_dir = d.split('@')
+            if d in self.widget.datalist._scanIDs:
+                send(scan_=self.widget.datalist._scanIDs[d])
             else:
-                entry = None,
-                scan_file_or_dir = d
-            try:
-                scan = ScanFactory.create_scan_object(scan_file_or_dir,
-                                                      entry=entry)
-            except Exception as e:
-                logger.error("Fail to create an instance of TomoBase from %s." \
-                             " Reason is %s" % (d, str(e)))
-            else:
-                send(scan_=scan)
+                logger.error('unable to retrieve scan {}'.format(d))
 
     @Inputs.data_in
     def add(self, scan):

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/reconstruction/AxisOW.py

@@ -133,6 +133,7 @@ class AxisOW(widget.OWWidget, WidgetLongProcessing):
         self._layout.addWidget(self._widget)
 
         # expose API
+        self.setMode = self._widget.setMode
         self.getAxis = self._widget.getAxis
         self.setValueLock = self._widget.setValueLock
         self._setModeLockFrmSettings = self._widget._setModeLockFrmSettings

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/reconstruction/NabuOW.py

@@ -66,7 +66,7 @@ class NabuOW(widget.OWWidget, OWClient, WidgetLongProcessing):
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = True
+    compress_signal = False
     allows_cycle = True
 
     _rpSetting = Setting(dict())
@@ -157,6 +157,7 @@ class NabuOW(widget.OWWidget, OWClient, WidgetLongProcessing):
             return
         scan_ = copy.copy(scan)
         scan_.clear_latest_reconstructions()
+        _logger.info('add {} to the stack'.format(str(scan)))
         self._processingStack.add(scan_, self.getConfiguration())
 
     @Inputs.reprocess
@@ -179,6 +180,7 @@ class NabuOW(widget.OWWidget, OWClient, WidgetLongProcessing):
         WidgetLongProcessing._endProcessing(self, scan)
         self.Outputs.data_out.send(scan)
         self.sigScanReady.emit(scan)
+        _logger.info('{} ended'.format(str(scan)))
 
     def setDryRun(self, dry_run):
         self._processingStack.setDryRun(dry_run)

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py

@@ -72,7 +72,7 @@ class NabuVolumeOW(widget.OWWidget, OWClient, WidgetLongProcessing):
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = True
+    compress_signal = False
     allows_cycle = True
 
     _rpSetting = Setting(dict())
@@ -160,13 +160,16 @@ class NabuVolumeOW(widget.OWWidget, OWClient, WidgetLongProcessing):
         if scan is None:
             return
         scan_ = copy.copy(scan)
-        scan_.clear_latest_reconstructions()
+        scan_.clear_latest_vol_reconstructions()
 
         # insure we are able to reconstruct
         if scan.nabu_recons_params in ({}, None):
             _logger.error('No reconstruction parameters found from nabu '
-                          'slices. You should first run slice '
-                          'reconstruction prior to volume reconstruction')
+                          'slices for {}. You should first run slice '
+                          'reconstruction prior to volume reconstruction'
+                          ''.format(str(scan)))
+            self.Outputs.data_out.send(scan)
+            self.sigScanReady.emit(scan)
             return
 
         config = scan.nabu_recons_params

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/reconstruction/test/test_axis.py

@@ -28,20 +28,22 @@ __date__ = "03/05/2019"
 
 
 from orangecontrib.tomwer.widgets.reconstruction.AxisOW import AxisOW
-from tomwer.test.utils import skip_gui_test
+from orangecontrib.tomwer.test.utils import OrangeWorflowTest
+from tomwer.test.utils import skip_gui_test, skip_orange_workflows_test
 from tomwer.test.utils import UtilsTest
 from tomwer.core.process.reconstruction.axis.mode import AxisMode
 from tomwer.core.settings import mock_lsbram
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core import utils
-from tomwer.core.utils.scanutils import MockEDF
+from tomwer.core.utils.scanutils import MockEDF, MockHDF5
 from silx.gui.utils.testutils import TestCaseQt
 from silx.gui import qt
+import numpy
 import shutil
 import tempfile
 import unittest
 import time
-import numpy
+import os
 
 
 @unittest.skipIf(skip_gui_test(), reason='skip gui test')
@@ -259,9 +261,87 @@ class TestAxisStack(TestCaseQt):
         self.assertEqual(self._scan3.axis_params.value, position_value)
 
 
+@unittest.skipIf(skip_orange_workflows_test(), reason='skip orange workflows tests')
+@unittest.skipIf(skip_gui_test(), reason='skip gui test')
+class AxisInWorkflow(OrangeWorflowTest):
+    """Test behavior of the axis widget with the following workflow:
+
+       * five HDF5Scan
+       * DataList -> Axis -> DataList
+       * Axis is set to the 'acccurate' algorithm and the processing is lock.
+
+    We make sure once the processing is finished each has a cor value and
+    end in the second DataList.
+    """
+
+    @classmethod
+    def setUpClass(cls):
+        OrangeWorflowTest.setUpClass()
+        # create widgets
+        cls.dataList1Node = cls.addWidget(cls,
+                                             'orangecontrib.tomwer.widgets.control.DataListOW.DataListOW')
+        cls.axisNode = cls.addWidget(cls,
+                                       'orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW')
+        cls.dataList2Node = cls.addWidget(cls,
+                                         'orangecontrib.tomwer.widgets.control.DataListOW.DataListOW')
+        cls.processOrangeEvents(cls)
+
+        cls.link(cls, cls.dataList1Node, "data", cls.axisNode, "data")
+        cls.link(cls, cls.axisNode, "data", cls.dataList2Node, "data")
+        cls.processOrangeEvents(cls)
+
+        cls.dataList1Widget = cls.getWidgetForNode(cls, cls.dataList1Node)
+        cls.axisWidget = cls.getWidgetForNode(cls, cls.axisNode)
+        cls.dataList2Widget = cls.getWidgetForNode(cls, cls.dataList2Node)
+
+        # Set we only want to simulate the reconstruction
+        cls.axisWidget.setMode('accurate')
+        cls.axisWidget._setModeLockFrmSettings(True)
+
+    def setUp(self):
+        OrangeWorflowTest.setUp(self)
+        self._source_dir = tempfile.mkdtemp()
+
+        def create_scan(folder_name):
+            _dir = os.path.join(self._source_dir, folder_name)
+            return MockHDF5(scan_path=_dir, n_ini_proj=10, n_proj=10,
+                            n_alignement_proj=2, create_final_ref=False,
+                            create_ini_dark=True, create_ini_ref=True,
+                            n_refs=1, dim=1000).scan
+
+        # create scans
+        self.scan_1 = create_scan('scan_1')
+        self.scan_2 = create_scan('scan_2')
+        self.scan_3 = create_scan('scan_3')
+        self.scan_4 = create_scan('scan_4')
+        self.scan_5 = create_scan('scan_5')
+        self.scans = [self.scan_1, self.scan_2, self.scan_3, self.scan_4,
+                      self.scan_5]
+
+    def tearDown(self):
+        shutil.rmtree(self._source_dir)
+        OrangeWorflowTest.tearDown(self)
+
+    def test(self):
+        """
+        Make sure if the scan receive 5 scan in 'normal way' then it will
+        compute axis for each of them and move then to the DataList
+        """
+        for scan in self.scans:
+            self.dataList1Widget.add(scan)
+
+        # start the workflow
+        self.dataList1Widget._sendList()
+        for i in range(10):
+            time.sleep(0.2)
+            self.app.processEvents()
+        self.assertEqual(self.dataList2Widget.n_scan(), 5)
+
+
 def suite():
     test_suite = unittest.TestSuite()
-    for ui in (TestOWAxis, TestWindowAxisComputation, TestAxisStack):
+    for ui in (TestOWAxis, TestWindowAxisComputation, TestAxisStack,
+               AxisInWorkflow):
         test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
     return test_suite
 

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/reconstruction/test/test_nabu_widget.py

@@ -36,6 +36,7 @@ import tempfile
 import unittest
 from silx.gui import qt
 from orangecontrib.tomwer.widgets.reconstruction.NabuOW import NabuOW
+from tomwer.core.utils.scanutils import MockHDF5
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.synctools.ftseries import QReconsParams
 from tomwer.test.utils import UtilsTest
@@ -43,6 +44,8 @@ from silx.gui.utils.testutils import TestCaseQt
 from silx.gui.utils.testutils import SignalListener
 from tomwer.core.settings import mock_lsbram
 from tomwer.core import utils
+from tomwer.test.utils import skip_gui_test, skip_orange_workflows_test
+from orangecontrib.tomwer.test.utils import OrangeWorflowTest
 from glob import glob
 import time
 
@@ -99,9 +102,83 @@ class TestNabuWidget(TestCaseQt):
         self.assertEqual(len(glob(os.path.join(self.scan_dir, '*.cfg'))), 0)
 
 
+@unittest.skipIf(skip_orange_workflows_test(), reason='skip orange workflows tests')
+@unittest.skipIf(skip_gui_test(), reason='skip gui test')
+class TestNabuWithBunchOfScan(OrangeWorflowTest):
+    """
+    Test the nabu widget with a bunch ot HDF5Scan and make sure all are
+    returner
+    """
+    """Test behavior of the axis widget with the following workflow:
+
+       * five HDF5Scan
+       * NabuReconstruction -> Axis -> DataList
+
+    We make sure once the processing is finished each has a cor value and
+    end in the second DataList.
+    """
+
+    @classmethod
+    def setUpClass(cls):
+        OrangeWorflowTest.setUpClass()
+        # create widgets
+        cls.dataList1Node = cls.addWidget(cls,
+                                             'orangecontrib.tomwer.widgets.control.DataListOW.DataListOW')
+        cls.axisNode = cls.addWidget(cls,
+                                       'orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW')
+        cls.dataList2Node = cls.addWidget(cls,
+                                         'orangecontrib.tomwer.widgets.control.DataListOW.DataListOW')
+        cls.processOrangeEvents(cls)
+
+        cls.link(cls, cls.dataList1Node, "data", cls.axisNode, "data")
+        cls.link(cls, cls.axisNode, "data", cls.dataList2Node, "data")
+        cls.processOrangeEvents(cls)
+
+        cls.dataList1Widget = cls.getWidgetForNode(cls, cls.dataList1Node)
+        cls.axisWidget = cls.getWidgetForNode(cls, cls.axisNode)
+        cls.dataList2Widget = cls.getWidgetForNode(cls, cls.dataList2Node)
+
+    def setUp(self):
+        OrangeWorflowTest.setUp(self)
+        self._source_dir = tempfile.mkdtemp()
+
+        def create_scan(folder_name):
+            _dir = os.path.join(self._source_dir, folder_name)
+            return MockHDF5(scan_path=_dir, n_ini_proj=10, n_proj=10,
+                            n_alignement_proj=2, create_final_ref=False,
+                            create_ini_dark=True, create_ini_ref=True,
+                            n_refs=1, dim=1000).scan
+
+        # create scans
+        self.scan_1 = create_scan('scan_1')
+        self.scan_2 = create_scan('scan_2')
+        self.scan_3 = create_scan('scan_3')
+        self.scan_4 = create_scan('scan_4')
+        self.scan_5 = create_scan('scan_5')
+        self.scans = [self.scan_1, self.scan_2, self.scan_3, self.scan_4,
+                      self.scan_5]
+        # TODO: add some dark and flat
+
+    def tearDown(self):
+        shutil.rmtree(self._source_dir)
+        OrangeWorflowTest.tearDown(self)
+
+    def test(self):
+        """
+        Make sure if the scan receive 5 scan in 'normal way' then it will
+        compute axis for each of them and move then to the DataList
+        """
+        for scan in self.scans:
+            self.dataList1Widget.add(scan)
+
+        # start the workflow
+        self.dataList1Widget._sendList()
+        self.assertEqual(self.dataList2Widget.n_scan(), 5)
+
+
 def suite():
     test_suite = unittest.TestSuite()
-    for ui in (TestNabuWidget, ):
+    for ui in (TestNabuWidget, TestNabuWithBunchOfScan):
         test_suite.addTest(
             unittest.defaultTestLoader.loadTestsFromTestCase(ui))
     return test_suite

users/payno/.local/share/virtualenvs/tomwer_venc/lib/python3.7/site-packages/tomwer/app/test/test_ows_to_script.py

@@ -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 tomwer.core.process.reconstruction.nabu import settings as nabu_settings
 from glob import glob
 import os
 
@@ -160,6 +161,7 @@ class TestDarkRefAxisNabu(unittest.TestCase, OwsScriptTest):
         self.entry = 'entry0000'
         self.scan = HDF5TomoScan(scan=self.master_file, entry=self.entry)
         self.script = os.path.join(self._data_dir, 'script.py')
+        self._nabu_cfg_dir = os.path.join(self._data_dir, nabu_settings.NABU_CFG_FILE_FOLDER)
 
     @staticmethod
     def get_scheme(file_path):
@@ -171,7 +173,7 @@ class TestDarkRefAxisNabu(unittest.TestCase, OwsScriptTest):
 
     def testProcessing_1(self):
         self.assertFalse(os.path.exists(self.tomwer_file))
-        self.assertEqual(len(glob(self.scan.path + os.sep + '*.cfg')), 0)
+        self.assertEqual(len(glob(self._nabu_cfg_dir + os.sep + '*.cfg')), 0)
         scheme_file = UtilsTest.getOrangeExecTestFile('darkref_axis_nabu.ows')
         self.scheme = self.get_scheme(scheme_file)
         # monkey patch parameters to use nabu in dry tun mode
@@ -203,11 +205,12 @@ class TestDarkRefAxisNabu(unittest.TestCase, OwsScriptTest):
             self.assertAlmostEqual(float(axp), (10. + 70.0), places=4)
             # +10: moved to nabu system (half width
         # check nabu files
-        self.assertEqual(len(glob(self._data_dir + os.sep + '*.cfg')), 2)
+        self.assertEqual(len(glob(self._nabu_cfg_dir + os.sep + '*.cfg')), 2)
 
     def testProcessing_2(self):
         self.assertFalse(os.path.exists(self.tomwer_file))
-        self.assertEqual(len(glob(self._data_dir + os.sep + '*.cfg')), 0)
+        self.assertEqual(len(glob(
+            os.path.join(self._nabu_cfg_dir, '*.cfg'))), 0)
 
         scheme_file = UtilsTest.getOrangeExecTestFile('darkref_axis_nabu_2.ows')
         self.scheme = self.get_scheme(scheme_file)
@@ -239,7 +242,7 @@ class TestDarkRefAxisNabu(unittest.TestCase, OwsScriptTest):
             self.assertAlmostEqual(float(axp), (10. + axis_cor), places=4)
             # +10: moved to nabu system (half width
         # check nabu files
-        self.assertEqual(len(glob(self._data_dir + os.sep + '*.cfg')), 2)
+        self.assertEqual(len(glob(self._nabu_cfg_dir + os.sep + '*.cfg')), 2)
 
 
 class TestPythonScript(unittest.TestCase, OwsScriptTest):