app - stitching: set the stitching output as a full path relative to the current working directory

close #1244

# Conflicts:
#	src/tomwer/app/stitching/common.py

# Conflicts:
#	src/tomwer/app/stitching/common.py

src/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__)

src/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

src/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:
@@ -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)

src/tomwer/gui/utils/inputwidget.py

@@ -437,7 +437,13 @@ 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(
+            os.path.join(
+                os.getcwd(),
+                "stitched_volume.hdf5",
+            ),
+            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)