tomwer 1.4.13__py3-none-any.whl → 1.4.14__py3-none-any.whl

tomwer/app/stitching/common.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import os
 import argparse
 import logging
 import signal
@@ -12,10 +13,10 @@ from tqdm import tqdm
 
 import silx
 from silx.gui import qt
+from silx.io.url import DataUrl
 
 from nabu.pipeline.config import generate_nabu_configfile
 from nabu.stitching.config import get_default_stitching_config, SECTIONS_COMMENTS
-import os
 from nabu.stitching.config import StitchingType
 
 from tomwer.core.volume.volumefactory import VolumeFactory
@@ -30,6 +31,8 @@ from tomwer.gui.stitching.StitchingWindow import YStitchingWindow as _YStitching
 from tomwer.gui.stitching import action as stitching_action
 from tomwer.gui.cluster.slurm import SlurmSettingsWidget
 from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.volume import HDF5Volume
 
 
 class MainWidget(qt.QTabWidget):
@@ -223,6 +226,26 @@ class MainWindow(qt.QDialog):
         self.layout().addWidget(self._buttons)
         self._buttons.button(qt.QDialogButtonBox.Apply).setText("Launch stitching")
 
+        # set up
+        self._mainWindow._stitchingConfigWindow.setPreProcessingOutput(
+            NXtomoScan(
+                scan=os.path.join(os.getcwd(), "stitching", "stitched.nx"),
+                entry="entry0000",
+            )
+            .get_identifier()
+            .to_str()
+        )
+        self._mainWindow._stitchingConfigWindow.setPostProcessingOutput(
+            HDF5Volume(
+                file_path=os.path.join(
+                    os.getcwd(), "stitching", "stitched_volume.hdf5"
+                ),
+                data_path="stitched_volume",
+            )
+            .get_identifier()
+            .to_str()
+        )
+
         # connect signal / slot
         self._buttons.button(qt.QDialogButtonBox.Apply).clicked.connect(self.accept)
         self._loadConfigurationAction.triggered.connect(
@@ -301,6 +324,12 @@ class MainWindow(qt.QDialog):
     def loadSettings(self, config_file: str):
         self._mainWindow.loadSettings(config_file)
 
+    def setPreProcessingOutput(self, url: DataUrl) -> None:
+        self._mainWindow._stitchingConfigWindow.setPreProcessingOutput(url=url)
+
+    def setPostProcessingOutput(self, url: DataUrl) -> None:
+        self._mainWindow._stitchingConfigWindow.setPostProcessingOutput(url=url)
+
 
 def main(argv, stitcher_name: str, stitching_axis: int, logger):
     parser = argparse.ArgumentParser(description=__doc__)

tomwer/gui/stitching/StitchingWindow.py

@@ -577,6 +577,12 @@ class _SingleAxisStitchingWindow(
             level >= ConfigurationLevel.ADVANCED
         )
 
+    def setPreProcessingOutput(self, *args, **kwargs):
+        self._outputWidget.setPreProcessingOutput(*args, **kwargs)
+
+    def setPostProcessingOutput(self, *args, **kwargs):
+        self._outputWidget.setPostProcessingOutput(*args, **kwargs)
+
 
 class YStitchingWindow(_SingleAxisStitchingWindow, axis=1):
     pass

tomwer/gui/stitching/config/output.py

@@ -9,6 +9,7 @@ from tomwer.core.scan.nxtomoscan import NXtomoScan, NXtomoScanIdentifier
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.gui.utils.inputwidget import OutputVolumeDefinition
 from tomwer.gui.qlefilesystem import QLFileSystem
+from silx.io.url import DataUrl
 
 _logger = logging.getLogger(__name__)
 
@@ -22,9 +23,9 @@ class _PreProcessingOutput(qt.QWidget):
         super().__init__(parent)
         self.setLayout(qt.QFormLayout())
         # TODO: check if the widget with output .nx file exists somewhere
-        self._outputFile = QLFileSystem("stitching/stitched.nx", self)
+        self._outputFile = QLFileSystem("", self)
         self.layout().addRow("output nexus file", self._outputFile)
-        self._outputDataPath = qt.QLineEdit("entry0000", self)
+        self._outputDataPath = qt.QLineEdit("", self)
         self.layout().addRow("output data path", self._outputDataPath)
 
     def getUrl(self) -> str:
@@ -114,8 +115,8 @@ class StitchingOutput(qt.QWidget):
                 scan = None
 
             if not isinstance(scan, NXtomoScan):
-                _logger.info("Failed to create an HDFTomoscan from url")
-                return None
+                _logger.warning("Failed to create an HDF5Tomoscan from url")
+                pass
             else:
                 config.update(
                     {
@@ -125,7 +126,7 @@ class StitchingOutput(qt.QWidget):
                         },
                     }
                 )
-                return config
+            return config
         else:
             raise NotImplementedError
 
@@ -160,3 +161,10 @@ class StitchingOutput(qt.QWidget):
         if overwrite is not None:
             overwrite = convert_str_to_bool(overwrite)
             self._overwritePB.setChecked(overwrite)
+
+    # expose API
+    def setPreProcessingOutput(self, identifier: str) -> None:
+        self._preProcOutput.setUrl(identifier)
+
+    def setPostProcessingOutput(self, identifier: DataUrl) -> None:
+        self._postProcOutput.setUrl(identifier)

tomwer/gui/utils/inputwidget.py

@@ -437,7 +437,7 @@ class OutputVolumeDefinition(qt.QWidget):
         # output file or folder
         self._outputFileLabel = qt.QLabel("", self)
         self.layout().addWidget(self._outputFileLabel, 1, 0, 1, 1)
-        self._outputFileQLE = QLFileSystem("stitched_volume.hdf5", parent=None)
+        self._outputFileQLE = QLFileSystem("", parent=None)
         self.layout().addWidget(self._outputFileQLE, 1, 1, 1, 1)
         self._selectPB = qt.QPushButton("select", self)
         self.layout().addWidget(self._selectPB, 1, 2, 1, 1)

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 4
-MICRO = 13
+MICRO = 14
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.4.13.dist-info → tomwer-1.4.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: tomwer
-Version: 1.4.13
+Version: 1.4.14
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone

{tomwer-1.4.13.dist-info → tomwer-1.4.14.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=WXL7Gs-dIkI2vjnOP_YZuiqF7OBdy5NZ4YivShSRyYk,4387
+tomwer/version.py,sha256=NdCYntfMNeKVf1OAvYXxI1EfJfcd4vMwcvkvuOXqN5s,4387
 tomwer/app/__init__.py,sha256=h1FKED7Tw5f99yikygt7ruXsdrxQhcJxO7kagLGxhJg,84
 tomwer/app/axis.py,sha256=lB-IZx1o6KTWLIelITvYCIu2flFTB9NhuIfD2MhUZZA,5826
 tomwer/app/canvas.py,sha256=y8rYOiwmv6ug7JcjgkOzEiGQnNXjKWNNmKofT0n8TFg,1538
@@ -252,7 +252,7 @@ tomwer/app/canvas_launcher/splash.py,sha256=cpUuZVKwlQbeAWfAqjpjP4q1v1MmkfxU6WWl
 tomwer/app/canvas_launcher/utils.py,sha256=WfsCHAhiiv4-TUNodgyKJenVvmFWnxsy5OBwTBK2jKE,1279
 tomwer/app/canvas_launcher/widgetsscheme.py,sha256=9Or1KMmSxIs_dJmJGV0Xhjg9HH4m8aPGbtiEuK2i6q0,2744
 tomwer/app/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tomwer/app/stitching/common.py,sha256=TCXNnAz2MSJrrogB5iWptktxq-g5ED2FUt_jMnDXpnQ,14723
+tomwer/app/stitching/common.py,sha256=-DNsE3XbBBCvm-NqSTCyJMiYY5GoGHkdzC0y66jZ6Po,15779
 tomwer/core/__init__.py,sha256=-EtD8J-a7WVnCgYS7WHkisYn61iM2PpHWcXwE5BetJ8,71
 tomwer/core/futureobject.py,sha256=8Sd9gOrdhYc0PvzPeZPBNOmaHuwB5epG6RJyABRsCmQ,5113
 tomwer/core/resourcemanager.py,sha256=VLNnVodMa-HOMZhN2qpUR_L6phJ8IHPUEPYMxuW6VHg,1067
@@ -600,7 +600,7 @@ tomwer/gui/samplemoved/__init__.py,sha256=jNA03mYWfP3_S1MRet6ijYe5DNCTK3Br7-5yrW
 tomwer/gui/samplemoved/selectiontable.py,sha256=CzQnJBxfIeoZSw8aR0VvrsaIg6fozREI8YRXdzQbA7Q,7968
 tomwer/gui/stitching/SingleAxisStitchingWidget.py,sha256=syBzSf8yRE9poZh0UKqZcyD8ZmEt-vama8bVRsGBuDw,13023
 tomwer/gui/stitching/StitchingOptionsWidget.py,sha256=c5kRZOMuGKK_CgK28IkBawaVvK2cmczbWF4TcVUZxq4,18186
-tomwer/gui/stitching/StitchingWindow.py,sha256=NlUX7htpS0BrlgBLeh_Mr5JpTzzyPVETU-j2_crQt20,24360
+tomwer/gui/stitching/StitchingWindow.py,sha256=g5lurZ3rZ010PBvU4oOWqDgcF3SbDzIqgIOyBHZ-Lyw,24608
 tomwer/gui/stitching/__init__.py,sha256=jYSG4DSAtMGm9Yuf4MVdlSdMO8JKOp_t-8NKsnR92LU,45
 tomwer/gui/stitching/action.py,sha256=7CkACYKsRt3c_6PgrmQVZwSi9UwvGrQVUymJytHbqcE,1659
 tomwer/gui/stitching/alignment.py,sha256=QGWnogvBSbx3kk8lrFDoipmhqbVHEe46WGAeOorlHQ8,4001
@@ -615,7 +615,7 @@ tomwer/gui/stitching/stitching_raw.py,sha256=imFJZyoVQ8H9JgdS02UoNcudvalfCQCAHVv
 tomwer/gui/stitching/utils.py,sha256=ZgfKHLyH7l81Ry-4M5ajdwqdeos_J4g4Ee3j3yoXcJo,599
 tomwer/gui/stitching/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/gui/stitching/config/axisparams.py,sha256=1cRa9ukPvVK7AGePJsJx2M_i_5TMLJocVwrotz7uxXk,8026
-tomwer/gui/stitching/config/output.py,sha256=sVmPQDMmFjmG5Dtuqy-805Qh8ZIbnDMgShnQOgjWQxQ,5936
+tomwer/gui/stitching/config/output.py,sha256=2kOKV5vTt1scIkmEUyhSvERRs8UvEHojRazCC0RzeE8,6176
 tomwer/gui/stitching/config/positionoveraxis.py,sha256=NGgjxzhxCXa3fBtHP9O9oiqLw8lpUqV_NNbhrnRGrdY,16328
 tomwer/gui/stitching/config/stitchingstrategies.py,sha256=BI5KYs0qeEp-hfFI7M9MJN8EHmoC7iaJqQ7Hf902v6Y,4598
 tomwer/gui/stitching/config/tomoobjdetails.py,sha256=GkQIqE2ArXFJFtmjrwc0txbZldNKJK-fpMEF_68S1qQ,14667
@@ -641,7 +641,7 @@ tomwer/gui/utils/completer.py,sha256=XQGVSiUdLa1MfgXPDY5qfcTxtjVerxmVKXmWDb-kQ-I
 tomwer/gui/utils/flow.py,sha256=p9KoaXSK_YhyFrpUTXr-HI1pAoDRiCPW1F9tVgjSIbA,10668
 tomwer/gui/utils/gpu.py,sha256=R2sRA77zyxdy5bVYGNltQpKS_9wuaj9eIn6rglsWGWg,2223
 tomwer/gui/utils/illustrations.py,sha256=SoLAGBIrdYAu44qIZM8kvC74naOTJzUyAxSUkpblyEw,3134
-tomwer/gui/utils/inputwidget.py,sha256=GXYIZdnVrBvWeXAY-nVBjD4rH5yXob3W35z0AA--qNA,22396
+tomwer/gui/utils/inputwidget.py,sha256=s1siEQ6nBOTVRF7v8wlgCISS0bYiVmWYpFnWCqM5ueY,22376
 tomwer/gui/utils/loadingmode.py,sha256=A9FeNacgnDFqhyrq5-qybCvV_NwGdXU-Skr_5vwoTZM,2928
 tomwer/gui/utils/qt_utils.py,sha256=QMXte_vdCEwr4Vybt5sopczQ_OuRd1W5h6SydqFH0F8,538
 tomwer/gui/utils/sandboxes.py,sha256=QfSRhL1KrFhS2Wr734Tzvp1OjTp82Ozc0ULr-JycFlI,6145
@@ -906,9 +906,9 @@ 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-1.4.13.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.4.13.dist-info/METADATA,sha256=D37N3t36794Bhflz9GYVqxpa__Uf_HHH48jSlHsdsxw,13416
-tomwer-1.4.13.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-tomwer-1.4.13.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.4.13.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.4.13.dist-info/RECORD,,
+tomwer-1.4.14.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
+tomwer-1.4.14.dist-info/METADATA,sha256=6cGCqNQ55Ns2Lu1E5zAiNPGjMAsN_8H0lfWsS0kctJ0,13416
+tomwer-1.4.14.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+tomwer-1.4.14.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
+tomwer-1.4.14.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
+tomwer-1.4.14.dist-info/RECORD,,