tomwer 1.3.27__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/app/samplemoved.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""Application to display a couple of projections at 180 degree and estimate (by eye) if a sample has moved
+"""
 
 import argparse
 import logging

tomwer/app/scanviewer.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""Application to browse a given scan
+"""
 
 import argparse
 import logging

tomwer/app/sinogramviewer.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""Application to display a sinogram from a scan
+"""
 
 import argparse
 import logging

tomwer/app/slicestack.py

@@ -1,11 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""Application to display findable reconstructed slice of a scan (as a stack).
+reconstructed slices can be added by hand or as input(s) of the command line.
+"""
 
 import argparse
 import logging
-import os
 import signal
 import sys
+import os
 
 import silx
 from silx.gui import qt
@@ -20,7 +23,7 @@ _logger = logging.getLogger(__name__)
 
 
 def getinputinfo():
-    return "tomwer slicestack [scanDir]"
+    return "tomwer slice-stack [scanDir]"
 
 
 def sigintHandler(*args):
@@ -28,18 +31,12 @@ def sigintHandler(*args):
     qt.QApplication.quit()
 
 
-def addFolderAndSubFolder(stack, path):
-    stack.addLeafScan(path)
-    for f in os.listdir(path):
-        _path = os.path.join(path, f)
-        if os.path.isdir(_path) is True:
-            addFolderAndSubFolder(stack, _path)
-
-
 def main(argv):
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument(
-        "root_dir", help="Root dir to browse and to extract all slices files under it."
+        "volume_paths",
+        help="Volumes to be added to the slice stack visualization. Warning: volumes should be single slice volumes.",
+        nargs="*",
     )
     parser.add_argument(
         "--use-opengl-plot",
@@ -80,8 +77,9 @@ def main(argv):
     splash = getMainSplashScreen()
     widget = SliceStack()
     widget.setWindowIcon(icons.getQIcon("tomwer"))
-    options.root_dir = options.root_dir.rstrip(os.path.sep)
-    addFolderAndSubFolder(stack=widget, path=options.root_dir)
+    widget._addTomoObjectsFromStrList(
+        [os.path.abspath(volume_path) for volume_path in options.volume_paths]
+    )
 
     splash.finish(widget)
     widget.show()

tomwer/app/stitching/common.py

@@ -0,0 +1,431 @@
+"""Common module for y and z stitcher"""
+
+from __future__ import annotations
+
+import argparse
+import logging
+import signal
+import sys
+import functools
+
+from tqdm import tqdm
+
+import silx
+from silx.gui import qt
+
+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
+from tomwer.core.settings import SlurmSettingsMode
+from tomwer.core.utils.resource import increase_max_number_file
+from tomwer.gui import icons
+from tomwer.core.process.stitching.nabustitcher import StitcherTask
+from tomwer.io.utils.tomoobj import get_tomo_objs_instances
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
+from tomwer.gui.stitching.StitchingWindow import ZStitchingWindow as _ZStitchingWindow
+from tomwer.gui.stitching.StitchingWindow import YStitchingWindow as _YStitchingWindow
+from tomwer.gui.stitching import action as stitching_action
+from tomwer.gui.cluster.slurm import SlurmSettingsWidget
+from tomwer.core.scan.scanbase import TomwerScanBase
+
+
+class MainWidget(qt.QTabWidget):
+    DEFAULT_NB_WORKERS = 10
+
+    def __init__(
+        self,
+        axis: int,
+        parent=None,
+    ) -> None:
+        super().__init__(parent)
+        if axis == 0:
+            self._stitchingConfigWindow = _ZStitchingWindow(
+                parent=self,
+                with_configuration_action=False,
+            )
+        elif axis == 1:
+            self._stitchingConfigWindow = _YStitchingWindow(
+                parent=self, with_configuration_action=False
+            )
+        else:
+            raise ValueError("stitching is only available along axis 0 and 1")
+
+        self.addTab(self._stitchingConfigWindow, "stitching config")
+        settingsClass = SlurmSettingsMode.get_settings_class(
+            SlurmSettingsMode.STITCHING
+        )
+        self._slurmConfig = SlurmSettingsWidget(
+            parent=self, n_gpu=settingsClass.N_GPUS_PER_WORKER, jobLimitation=None
+        )
+        self._slurmConfig.setConfiguration(
+            {
+                "cpu-per-task": settingsClass.N_CORES_PER_TASK,
+                "n_tasks": settingsClass.N_TASKS,
+                "n_jobs": settingsClass.N_JOBS,
+                "memory": settingsClass.MEMORY_PER_WORKER,
+                "partition": settingsClass.PARTITION,
+                "n_gpus": settingsClass.N_GPUS_PER_WORKER,
+                "job_name": settingsClass.PROJECT_NAME,
+                "python_venv": settingsClass.PYTHON_VENV,
+            }
+        )
+
+        self._stitchingConfigWindow.setCallbackToGetSlurmConfig(
+            self._slurmConfig.getConfiguration
+        )
+        self._stitchingConfigWindow.setCallbackToSetSlurmConfig(
+            self._slurmConfig.setConfiguration
+        )
+        self.addTab(self._slurmConfig, "slurm config")
+        # add an option to clearly activate / deactivate slurm config
+        slurm_config_idx = self.indexOf(self._slurmConfig)
+        self._slurmCB = qt.QCheckBox(self)
+        self.tabBar().setTabButton(
+            slurm_config_idx,
+            qt.QTabBar.LeftSide,
+            self._slurmCB,
+        )
+        self._slurmCB.setChecked(True)
+
+        # set up
+        self._slurmConfig.setNWorkers(self.DEFAULT_NB_WORKERS)
+
+    def close(self):
+        self._stitchingConfigWindow.close()
+        # requested for the waiting plot update
+        super().close()
+
+    def keyPressEvent(self, event):
+        """
+        To shortcut orange and make sure the `F5` <=> refresh stitching preview
+        """
+        modifiers = event.modifiers()
+        key = event.key()
+
+        if key == qt.Qt.Key_F5:
+            self._stitchingConfigWindow._trigger_update_preview()
+        elif key == qt.Qt.Key_O and modifiers == qt.Qt.KeyboardModifier.ControlModifier:
+            self._stitchingConfigWindow._loadSettings()
+        elif key == qt.Qt.Key_S and modifiers == qt.Qt.KeyboardModifier.ControlModifier:
+            self._stitchingConfigWindow._saveSettings()
+
+    def getStitchingConfiguration(self) -> dict:
+        return self._stitchingConfigWindow.getConfiguration()
+
+    def getClusterConfig(self) -> dict:
+        return self._slurmConfig.getConfiguration()
+
+    # expose API
+    def addTomoObj(self, *args, **kwargs):
+        self._stitchingConfigWindow.addTomoObj(*args, **kwargs)
+
+    def setStitchingType(self, stitching_type):
+        self._stitchingConfigWindow.setStitchingType(stitching_type)
+
+    def loadSettings(self, config_file):
+        self._stitchingConfigWindow._loadSettings(config_file)
+
+
+class _StitcherThread(qt.QThread):
+    DEFAULT_OUTPUT_CONFIG_NAME = "stitching_conf_autosave.conf"
+
+    def __init__(self, parent, stitching_config, cluster_config) -> None:
+        super().__init__(parent)
+        assert isinstance(stitching_config, dict)
+        assert isinstance(cluster_config, dict)
+        self._stitching_config = stitching_config
+        self._cluster_config = cluster_config
+
+    def save_configuration(self):
+        stitching_type = self._stitching_config["stitching"]["type"]
+        if "preproc" in stitching_type:
+            output_file = self._stitching_config.get("preproc", {}).get("location", "")
+            output_folder = os.path.dirname(output_file)
+        else:
+            output_volume = self._stitching_config.get("postproc", {}).get(
+                "output_volume", None
+            )
+            if output_volume is None:
+                output_folder = ""
+            else:
+                volume = VolumeFactory.create_tomo_object_from_identifier(output_volume)
+                output_folder = os.path.dirname(volume.data_url.file_path())
+
+        os.makedirs(output_folder, exist_ok=True)
+        generate_nabu_configfile(
+            fname=os.path.join(
+                output_folder,
+                _StitcherThread.DEFAULT_OUTPUT_CONFIG_NAME,
+            ),
+            default_config=get_default_stitching_config(
+                self._stitching_config["stitching"]["type"]
+            ),
+            comments=True,
+            sections_comments=SECTIONS_COMMENTS,
+            options_level="advanced",
+            prefilled_values=self._stitching_config,
+        )
+
+    def run(self):
+        self.save_configuration()
+
+        task = StitcherTask(
+            inputs={
+                "stitching_config": self._stitching_config,
+                "cluster_config": self._cluster_config,
+                "progress": tqdm(desc="stitching"),
+                "serialize_output_data": False,
+            },
+        )
+
+        if self._cluster_config in (None, {}):
+            self._runLocally(task)
+        else:
+            self._runRemotely(task)
+
+    def _runLocally(self, task):
+        task.run()
+
+    def _runRemotely(self, task):
+        task.run()
+        # wait for processing to be finished
+        for future in task.outputs.future_tomo_obj.futures:
+            future.result()
+        # note: there is also a callback to aggregate result once all are finished.
+        # so at this stage the final "nxtomo" or "volume" might not exists yet
+
+
+class MainWindow(qt.QDialog):
+    def __init__(self, axis: int, parent=None) -> None:
+        super().__init__(parent)
+        self.setLayout(qt.QVBoxLayout())
+        # menu
+        self._menuBar = qt.QMenuBar(self)
+        self.layout().addWidget(self._menuBar)
+        self._menu = qt.QMenu("&Stitching")
+        self._menuBar.addMenu(self._menu)
+        # save / load configuration
+        self._loadConfigurationAction = stitching_action.LoadConfigurationAction(
+            self, "&Load configuration"
+        )
+        self._menu.addAction(self._loadConfigurationAction)
+        self._saveConfigurationAction = stitching_action.SaveConfigurationAction(
+            self, "&Save configuration"
+        )
+        self._menu.addAction(self._saveConfigurationAction)
+        # separator
+        self._menu.addSeparator()
+        # add tomo object
+        self._addTomoObjectAction = stitching_action.AddTomoObjectAction(
+            self, "&Add tomo object (volume or NXtomo)"
+        )
+        self._menu.addAction(self._addTomoObjectAction)
+
+        # main window
+        self.setWindowTitle("tomwer z-stitching")
+        self._mainWindow = MainWidget(parent=self, axis=axis)
+        self.layout().addWidget(self._mainWindow)
+
+        # button
+        types = qt.QDialogButtonBox.Apply
+        self._buttons = qt.QDialogButtonBox(self)
+        self._buttons.setStandardButtons(types)
+        self.layout().addWidget(self._buttons)
+        self._buttons.button(qt.QDialogButtonBox.Apply).setText("Launch stitching")
+
+        # connect signal / slot
+        self._buttons.button(qt.QDialogButtonBox.Apply).clicked.connect(self.accept)
+        self._loadConfigurationAction.triggered.connect(
+            functools.partial(
+                self._mainWindow._stitchingConfigWindow._loadSettings, file_path=None
+            )
+        )
+        self._saveConfigurationAction.triggered.connect(
+            functools.partial(
+                self._mainWindow._stitchingConfigWindow._saveSettings, file_path=None
+            )
+        )
+        self._addTomoObjectAction.triggered.connect(self._callbackAddTomoObj)
+
+    def _callbackAddTomoObj(self, *args, **kwargs):
+        """move interface to the z-ordered list and call the 'add tomo obj' callback"""
+        orderedListWidget = (
+            self._mainWindow._stitchingConfigWindow._widget._mainWidget._axisOrderedList
+        )
+        self._mainWindow._stitchingConfigWindow._widget._mainWidget.setCurrentWidget(
+            orderedListWidget
+        )
+        orderedListWidget._callbackAddTomoObj()
+
+    def close(self):
+        self._mainWindow.close()
+        # requested for the waiting plot update
+        super().close()
+
+    def reject(self):
+        self.close()
+        super().reject()
+
+    def accept(self):
+        self.process_stitching()
+
+    def process_stitching(self):
+        self._processingThread = _StitcherThread(
+            parent=self,
+            stitching_config=self.getStitchingConfiguration(),
+            cluster_config=self.getClusterConfig(),
+        )
+        self._processingThread.start()
+
+    def disableSlurmconfig(self):
+        self._mainWindow._slurmCB.setChecked(False)
+        self._mainWindow._slurmCB.setCheckable(False)
+
+        slurm_config_idx = self._mainWindow.indexOf(self._mainWindow._slurmConfig)
+
+        self._mainWindow.setTabEnabled(
+            slurm_config_idx,
+            False,
+        )
+        self._mainWindow.setTabToolTip(
+            slurm_config_idx,
+            "not available because unable to find slurm command (computer is probably not a slurm client ?",
+        )
+
+    # expose API
+    def addTomoObj(self, *args, **kwargs):
+        self._mainWindow.addTomoObj(*args, **kwargs)
+
+    def getClusterConfig(self) -> dict:
+        if self._mainWindow._slurmCB.isChecked():
+            return self._mainWindow.getClusterConfig()
+        else:
+            return {}
+
+    def getStitchingConfiguration(self) -> dict:
+        return self._mainWindow.getStitchingConfiguration()
+
+    def setStitchingType(self, stitching_type):
+        self._mainWindow.setStitchingType(stitching_type)
+
+    def loadSettings(self, config_file: str):
+        self._mainWindow.loadSettings(config_file)
+
+
+def main(argv, stitcher_name: str, stitching_axis: int, logger):
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument(
+        "tomo_objs",
+        help="All tomo objects to be stitched together",
+        nargs="*",
+    )
+    parser.add_argument(
+        "--debug",
+        dest="debug",
+        action="store_true",
+        default=False,
+        help="Set logging system in debug mode",
+    )
+
+    parser.add_argument(
+        "--config",
+        "--config-file",
+        dest="config_file",
+        default=None,
+        help="Provide stitching configuration file to load parameters from it",
+    )
+    parser.add_argument(
+        "--use-opengl-plot",
+        help="Use OpenGL for plots (instead of matplotlib)",
+        action="store_true",
+        default=False,
+    )
+    parser.add_argument(
+        "--check-scans",
+        help="If True will check scans before adding them. This check scan validity (virtual dataset contains data...)",
+        action="store_true",
+        default=False,
+    )
+    options = parser.parse_args(argv[1:])
+
+    if options.use_opengl_plot:
+        silx.config.DEFAULT_PLOT_BACKEND = "gl"
+    else:
+        silx.config.DEFAULT_PLOT_BACKEND = "matplotlib"
+
+    if options.debug:
+        logging.root.setLevel(logging.DEBUG)
+
+    increase_max_number_file()
+
+    global app  # QApplication must be global to avoid seg fault on quit
+    app = qt.QApplication.instance() or qt.QApplication(["tomwer"])
+    splash = getMainSplashScreen()
+    qt.QApplication.processEvents()
+
+    qt.QLocale.setDefault(qt.QLocale(qt.QLocale.English))
+    qt.QLocale.setDefault(qt.QLocale.c())
+    signal.signal(signal.SIGINT, sigintHandler)
+    sys.excepthook = qt.exceptionHandler
+
+    timer = qt.QTimer()
+    timer.start(500)
+    # Application have to wake up Python interpreter, else SIGINT is not
+    # catch
+    timer.timeout.connect(lambda: None)
+
+    window = MainWindow(axis=stitching_axis)
+    window.setWindowFlags(qt.Qt.Window)
+    window.setWindowTitle(stitcher_name)
+    window.setWindowIcon(icons.getQIcon("tomwer"))
+
+    window.show()
+    from sluurp.utils import has_sbatch_available
+
+    # load configuration is some provided
+    if options.config_file is not None:
+        window.loadSettings(options.config_file)
+
+    if not has_sbatch_available():
+        window.disableSlurmconfig()
+
+    tomo_objs, (has_scans, has_vols) = get_tomo_objs_instances(options.tomo_objs)
+    for tomo_obj in tomo_objs:
+        if isinstance(tomo_obj, TomwerScanBase):
+            tomo_obj.set_check_behavior(
+                run_check=options.check_scans
+            )  # speed up processing
+        window.addTomoObj(tomo_obj=tomo_obj)
+    if has_scans and has_vols:
+        logger.warning(
+            "seems like you have both volumes and scan on your inputs. Unable to stitch the two at the same time"
+        )
+    elif has_scans:
+        if stitching_axis == 0:
+            window.setStitchingType(StitchingType.Z_PREPROC)
+        elif stitching_axis == 1:
+            window.setStitchingType(StitchingType.Y_PREPROC)
+        else:
+            raise ValueError(
+                f"stitching on scans is not possible along the axis {stitching_axis} (must be 0 or 1)"
+            )
+    elif has_vols:
+        if stitching_axis == 0:
+            window.setStitchingType(StitchingType.Z_POSTPROC)
+        else:
+            raise ValueError(
+                f"stitching on volumes is not possible along the axis {stitching_axis} (must be 0). Should be possible in theory. Please contact us so we can have a dataset and test it"
+            )
+
+    window.setAttribute(qt.Qt.WA_DeleteOnClose)
+    splash.finish(window)
+    exit(app.exec_())
+
+
+def sigintHandler(*args):
+    """Handler for the SIGINT signal."""
+    qt.QApplication.closeAllWindows()  # needed because get a waiting thread behind
+    qt.QApplication.quit()

tomwer/app/stopdatalistener.py

@@ -1,5 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""
+Application to stop possible running data listener (and free used port)
+"""
 
 import argparse
 import sys

tomwer/app/ystitching.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Application to stitch along y (aka axis 0) a set of scans or reconstructed volumes
+"""
+from __future__ import annotations
+
+import sys
+import logging
+from tomwer.app.stitching.common import main as common_main
+
+logging.basicConfig(level=logging.WARNING)
+
+_logger = logging.getLogger(__name__)
+
+
+def getinputinfo():
+    return "tomwer y-stitching [tomo objects]"
+
+
+def main(argv):
+    common_main(argv, stitcher_name="y-stitching", stitching_axis=1, logger=_logger)
+
+
+if __name__ == "__main__":
+    main(sys.argv)