dcscope 2.27.0__tar.gz → 2.28.1__tar.gz

{dcscope-2.27.0 → dcscope-2.28.1}/.github/workflows/deploy_github.yml

@@ -34,6 +34,9 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
         pip install .
+        # https://github.com/DC-analysis/DCscope/issues/228
+        # install pyqtgraph > 0.14.0 fixing SVG export issue
+        pip install git+https://github.com/pyqtgraph/pyqtgraph.git@4683d7a2d3f2b0a8412618a41dc780bd9cce339b
     - name: Build windows executable
       if: runner.os == 'windows'
       working-directory: ./build-recipes

{dcscope-2.27.0 → dcscope-2.28.1}/CHANGELOG

@@ -1,3 +1,38 @@
+2.28.1
+ - reg: limits of box filters incorrectly shown when QuickView was active
+ - enh: `Pipeline.get_min_max_coarse` handles inf data
+ - enh: align-right box filter selection button in Analysis View
+ - enh: disable "Apply" button when changing box filters in Analysis View
+ - build: include latest version of pyqtgraph to fix SVG export issue (#228)
+2.28.0
+ - feat: introduce `TaskManager` and `TaskWorker` for more progress bars
+ - fix: plot resized when applying plot settings in AnalysisView
+ - fix: memory leak in plotting (plot elements were not removed)
+ - fix: KDE contour spacing test only done on largest percentile contour
+ - fix: deleting last filter in Analysis View caused `IndexError`
+ - fix: deleting last plot in Analysis View caused `IndexError`
+ - reg: subplot export via context menu did not work
+ - reg: dot-menu for plot matrix element removed in refactoring process
+ - enh: show number of tasks running in status bar
+ - enh: migrate data file export to `Taskmanager`
+ - enh: show progress bar when opening a session (uses `Taskmanager`)
+ - enh: enable rubberband-resize for all subwindows
+ - enh: maximize main window before loading session
+ - enh: streamline session loading (remove duplicate plotting calls)
+ - enh: move plot data checking to background thread
+ - enh: dark mode icons (#226)
+ - setup: bump dclab to 0.71.9 (thread-safety for filtering)
+ - docs: update screenshots (and recipes)
+ - ref: scatter plot data generation done in background thread
+ - ref: contour plot data generation done in background thread
+ - ref: use `TaskManager` for computing plot data in QuickView
+ - ref: cleanup main.py, session.py with the help of pyright
+ - ref: move custom colorbar definitions to `colorbaritem`
+ - ref: put heavy-duty plotting code into `pipeline_plot_compute`
+ - ref: separate PipelinePlotItem into its own submodule
+ - ref: compute brush color in background thread alongside KDE
+ - ref: `zoomin_contours` calls `compute_contours_from_state` unneccesarily
+ - tests: update manual tests session with correct contour spacing
 2.27.0
  - fix: delay on selecting "Plot" tab when "Marker hue" was set to "Feature"
  - fix: switching tabs "View/Features" in QuickView did not update event data

{dcscope-2.27.0/dcscope.egg-info → dcscope-2.28.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcscope
-Version: 2.27.0
+Version: 2.28.1
 Summary: User interface for deformability cytometry (DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -16,7 +16,7 @@ Classifier: Intended Audience :: Science/Research
 Requires-Python: <4,>=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: dclab[dcor,export,http,s3]>=0.71.7
+Requires-Dist: dclab[dcor,export,http,s3]>=0.71.9
 Requires-Dist: h5py>=2.8.0
 Requires-Dist: numpy>=1.21
 Requires-Dist: pygments

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/__main__.py

@@ -1,14 +1,33 @@
 def main(splash=True):
     import importlib.resources
     import sys
+    import warnings
 
     from PyQt6.QtWidgets import QApplication
-    from PyQt6.QtCore import QEventLoop
+    from PyQt6.QtCore import QEventLoop, Qt
+    from PyQt6 import QtGui
     # import before creating application
     import pyqtgraph  # noqa: F401
 
     app = QApplication(sys.argv)
 
+    style_hints = QApplication.styleHints()
+    if style_hints.colorScheme() == Qt.ColorScheme.Dark:
+        theme_shade = "dark"
+    else:
+        theme_shade = "light"
+
+    # set Qt icon theme search path
+    ref = importlib.resources.files("dcscope.img") / "icon.png"
+    with importlib.resources.as_file(ref) as icon_path:
+        theme_dir = icon_path.with_name("icon-theme")
+        theme_path = theme_dir / theme_shade
+    if theme_path.exists():
+        QtGui.QIcon.setThemeSearchPaths([str(theme_path)])
+        QtGui.QIcon.setThemeName(".")
+    else:
+        warnings.warn("DCscope theme path not available")
+
     if splash:
         from PyQt6.QtWidgets import QSplashScreen
         from PyQt6.QtGui import QPixmap

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '2.27.0'
-__version_tuple__ = version_tuple = (2, 27, 0)
+__version__ = version = '2.28.1'
+__version_tuple__ = version_tuple = (2, 28, 1)
 
-__commit_id__ = commit_id = 'g762a62993'
+__commit_id__ = commit_id = 'g204651dbc'

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/gui/analysis/ana_filter.py

@@ -293,6 +293,11 @@ class FilterPanel(QtWidgets.QWidget):
                     filt_index = None
                 self.update_content(filt_index)
 
+                filt_rem = pp_dict.get("filter_removed")
+                if filt_rem is not None:
+                    # remove filter item from list/view
+                    self.update_content()
+
         qv_dict = data.get("quickview")
         if qv_dict and qv_dict.get("enabled"):
             if self.isVisible():
@@ -316,6 +321,7 @@ class FilterPanel(QtWidgets.QWidget):
     def on_moreless(self):
         """User wants to choose box filters"""
         if not self._box_edit_view:
+            self.ui.pushButton_apply.setEnabled(False)
             # get available features to show
             features, _ = self.get_features_labels()
             # create missing range controls if applicable (e.g. ml_score_???)
@@ -332,6 +338,7 @@ class FilterPanel(QtWidgets.QWidget):
             self.ui.label_box_edit.setVisible(True)
             self._box_edit_view = True
         else:
+            self.ui.pushButton_apply.setEnabled(True)
             # Hide all filters that are not active
             for _, rc in self._box_range_controls.items():
                 if not rc.is_active():
@@ -359,11 +366,14 @@ class FilterPanel(QtWidgets.QWidget):
         if self.pipeline and self.pipeline.filters:
             # remember the previous filter index and make sure it is sane
             prev_index = self.ui.comboBox_filters.currentIndex()
-            if prev_index is None or prev_index < 0:
+            if (
+                prev_index is None
+                or prev_index < 0
+                or prev_index > len(self.filter_ids) - 1
+            ):
                 prev_index = len(self.filter_ids) - 1
 
             self.setEnabled(True)
-            self.update_polygon_filters()
             # update combobox
             self.ui.comboBox_filters.blockSignals(True)
             if filt_index is None or filt_index < 0:
@@ -376,6 +386,9 @@ class FilterPanel(QtWidgets.QWidget):
                 [filt.name for filt in self.pipeline.filters])
             self.ui.comboBox_filters.setCurrentIndex(filt_index)
             self.ui.comboBox_filters.blockSignals(False)
+
+            self.update_polygon_filters()
+
             # populate content
             filt = self.pipeline.filters[filt_index]
             state = filt.__getstate__()
@@ -393,12 +406,14 @@ class FilterPanel(QtWidgets.QWidget):
             # compute min/max values
             mmdict = {}
             for feat in self.active_box_features:
-                mmdict[feat] = self.pipeline.get_min_max(feat=feat)
+                mmdict[feat] = self.pipeline.get_min_max_coarse(feat=feat)
             # update used features
             for feat in self._box_range_controls:
                 rc = self._box_range_controls[feat]
                 if feat in mmdict:
                     rc.setLimits(*mmdict[feat])
+                else:
+                    print("Ignoring feature", feat)
                 if self.current_filter is not None:
                     state = self.current_filter.__getstate__()
                     if feat not in state["box filters"]:

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/gui/analysis/ana_filter_ui.py

@@ -118,7 +118,7 @@ class Ui_Form(object):
         self.verticalLayout_3.addWidget(self.label_box_edit)
         self.toolButton_moreless = QtWidgets.QToolButton(parent=self.groupBox_box)
         self.toolButton_moreless.setObjectName("toolButton_moreless")
-        self.verticalLayout_3.addWidget(self.toolButton_moreless)
+        self.verticalLayout_3.addWidget(self.toolButton_moreless, 0, QtCore.Qt.AlignmentFlag.AlignRight)
         self.verticalLayout_5.addWidget(self.groupBox_box)
         self.groupBox = QtWidgets.QGroupBox(parent=Form)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Minimum)

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/gui/analysis/ana_plot.py

@@ -556,6 +556,8 @@ class PlotPanel(QtWidgets.QWidget):
                 else:
                     plot_index = None
                 self.update_content(plot_index)
+            elif pp_dict.get("plot_removed"):
+                self.update_content()
             elif pp_dict.get("plot_changed") == self.current_plot.identifier:
                 self.update_content()
 
@@ -649,7 +651,11 @@ class PlotPanel(QtWidgets.QWidget):
         if self._pipeline is not None and self.plot_ids:
             # remember the previous plot index and make sure it is sane
             prev_index = self.ui.comboBox_plots.currentIndex()
-            if prev_index is None or prev_index < 0:
+            if (
+                prev_index is None
+                or prev_index < 0
+                or prev_index > len(self.plot_ids) - 1
+            ):
                 prev_index = len(self.plot_ids) - 1
 
             self.setEnabled(True)

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/gui/export/e2data.py

@@ -1,6 +1,8 @@
 import logging
 import pathlib
+import threading
 import traceback
+from typing import Callable
 
 from PyQt6 import QtCore, QtTest, QtWidgets
 
@@ -8,6 +10,7 @@ import dclab
 
 from ...util import get_valid_filename
 from ..._version import version
+from ..tasks import TaskManager, TaskAbortError
 from ..widgets import get_directory, show_wait_cursor
 from ..widgets.feature_combobox import HIDDEN_FEATURES
 from .e2data_ui import Ui_Dialog
@@ -138,6 +141,8 @@ class ExportData(QtWidgets.QDialog):
         else:
             features = self.ui.bulklist_features.get_selection()
 
+        tm = TaskManager(self)
+
         # create dummy progress dialog
         prog = QtWidgets.QProgressDialog("Exporting...", "Abort", 1,
                                          10, self)
@@ -156,7 +161,7 @@ class ExportData(QtWidgets.QDialog):
         QtWidgets.QApplication.processEvents(
             QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 300)
 
-        tasks = []
+        jobs = []
 
         for slot_index, path in slots_n_paths:
             ds = self.pipeline.get_dataset(slot_index)
@@ -174,7 +179,7 @@ class ExportData(QtWidgets.QDialog):
                      + f"They are not exported to .{self.file_format}!")
                 )
             if self.file_format == "rtdc":
-                tasks.append((
+                jobs.append((
                     ds.export.hdf5,
                     dict(path=path,
                          features=[ff for ff in features if ff in ds.features],
@@ -185,7 +190,7 @@ class ExportData(QtWidgets.QDialog):
                          override=False)
                 ))
             elif self.file_format == "fcs":
-                tasks.append((
+                jobs.append((
                     ds.export.fcs,
                     dict(path=path,
                          features=[ff for ff in features if ff in ds.features],
@@ -193,7 +198,7 @@ class ExportData(QtWidgets.QDialog):
                          override=False)
                 ))
             elif self.file_format == "tsv":
-                tasks.append((
+                jobs.append((
                     ds.export.tsv,
                     dict(path=path,
                          features=[ff for ff in features if ff in ds.features],
@@ -201,43 +206,52 @@ class ExportData(QtWidgets.QDialog):
                          override=False)
                 ))
             elif self.ui.radioButton_avi.isChecked():
-                tasks.append((
+                jobs.append((
                     ds.export.avi,
                     dict(path=path,
                          **self.ui.comboBox_codec.currentData())
                 ))
 
-        logger.info(f"Exporting {len(tasks)} objects")
-
-        exporter = ExportThread(self, tasks)
-        exporter.communicate_progress.connect(prog.setValue)
-        exporter.communicate_message.connect(prog.setLabelText)
-        prog.canceled.connect(exporter.request_abort)
-        exporter.start()
+        logger.info(f"Exporting {len(jobs)} objects")
+
+        task = {"func": perform_export,
+                "args": [],
+                "kwargs": {"jobs": jobs}
+                }
+        tm.add_task(
+            task=task,
+            topic="export",
+            communicate_progress=prog.setValue,
+            communicate_message=prog.setLabelText,
+        )
 
         while True:
-            QtWidgets.QApplication.processEvents(
-                QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 300)
             QtTest.QTest.qWait(500)
-            if prog.wasCanceled() or exporter.isFinished():
-                # This will break the loop but possibly keep the exporter
-                # alive. We hope that the exporter will eventually be
-                # terminated.
+            if prog.wasCanceled():
+                tm.abort_task(task)
+                while tm.is_task_running(task):
+                    # force user to wait until the task properly aborted
+                    prog.show()
+                    prog.setLabelText("Aborting, please wait...")
+                    prog.setMaximum(0)
+                    prog.setMinimum(0)
+                    QtTest.QTest.qWait(500)
+                break
+            elif tm.is_task_finished(task):
+                result = tm.get_task_result(task)
+                if result["jobs_failed"]:
+                    info_string = "\n".join(
+                        [f"- {kw['path']}" for _, kw in result["jobs_failed"]])
+                    QtWidgets.QMessageBox.critical(
+                        self,
+                        f"Error exporting {len(result['jobs_failed'])} "
+                        f"datasets",
+                        f"Could not export to the following "
+                        f"paths:\n{info_string}")
                 break
 
-        prog.setValue(pend)
-
-        if prog.wasCanceled():
-            exporter.terminate()
-        else:
-            exporter.wait()
-
-        if exporter.failed_tasks:
-            info_string = "\n".join(
-                [f"- {kw['path']}" for _, kw in exporter.failed_tasks])
-            QtWidgets.QMessageBox.critical(
-                self, f"Error exporting {len(exporter.failed_tasks)} objects",
-                f"Could not export to the following paths:\n{info_string}")
+        prog.deleteLater()
+        tm.close()
 
     def get_export_filenames(self):
         """Compute names for exporting data, avoiding overriding anything
@@ -350,52 +364,62 @@ class ExportData(QtWidgets.QDialog):
         self.on_select_features_innate()
 
 
-class ExportAbortError(BaseException):
-    """Used for aborting data export via progress_callback"""
-    pass
-
-
-class ExportThread(QtCore.QThread):
-    communicate_progress = QtCore.pyqtSignal(int)
-    communicate_message = QtCore.pyqtSignal(str)
-
-    def __init__(self, parent, tasks):
-        super(ExportThread, self).__init__(parent)
-        self.abort = False
-        self.tasks = tasks
-        self.current_path = None
-        self.tasks_done = []
-        self.failed_tasks = []
-        self.setObjectName(self.__class__.__name__)
-
-    def progress_callback(self, progress, message):
-        cur_pos = int((len(self.tasks_done) + progress) * 100)
-        self.communicate_progress.emit(cur_pos)
-        self.communicate_message.emit(f"{self.current_path.name} ({message})")
-        if self.abort:
-            raise ExportAbortError("User aborted")
-
-    def run(self):
-        for ii in range(len(self.tasks)):
-            if self.abort:
-                break
-            func, kwargs = self.tasks.pop(0)
-            self.current_path = pathlib.Path(kwargs["path"])
-            try:
-                func(progress_callback=self.progress_callback, **kwargs)
-            except ExportAbortError:
-                # remove current path
-                self.current_path.unlink(missing_ok=True)
-                break
-            except BaseException:
-                # remove current path
-                self.current_path.unlink(missing_ok=True)
-                logger.error(traceback.format_exc())
-                self.failed_tasks.append((func, kwargs))
-                continue
-            finally:
-                self.tasks_done.append((func, kwargs))
+def perform_export(jobs: list[tuple[Callable, dict]],
+                   communicate_progress: Callable,
+                   communicate_message: Callable,
+                   event_abort: threading.Event
+                   ) -> dict[str, list[tuple[Callable, dict]]]:
+    """Perform data export
+
+    Parameters
+    ----------
+    jobs:
+        list of job dictionaries. Each job consists of a callable and the
+        corresponding keyword arguments.
+    communicate_progress:
+        method for communicating the overall progress
+        (used for progress bar)
+    communicate_message:
+        method for communicating the current progress message
+        (used for progress bar)
+    event_abort:
+        an event that can be set to abort the export
+
+    Returns
+    -------
+    result:
+        dictionary with "jobs_done" and "jobs_failed" lists
+    """
+    jobs_failed = []
+    jobs_done = []
+
+    def handle_export_progress(idx, progress, message):
+        communicate_progress(int((idx + progress)*100))
+        communicate_message(message)
+
+    for ii in range(len(jobs)):
+        if event_abort.is_set():
+            break
+        func, kwargs = jobs.pop(0)
+        current_path = pathlib.Path(kwargs["path"])
+        try:
+            func(progress_callback=lambda p, m: (
+                    handle_export_progress(ii, p, m)),
+                 **kwargs)
+        except TaskAbortError:
+            # cleanup: remove current path
+            current_path.unlink(missing_ok=True)
+            raise
+        except BaseException:
+            # remove current path
+            current_path.unlink(missing_ok=True)
+            logger.error(traceback.format_exc())
+            jobs_failed.append((func, kwargs))
+            continue
+        else:
+            jobs_done.append((func, kwargs))
 
-    @QtCore.pyqtSlot()
-    def request_abort(self):
-        self.abort = True
+    return {
+        "jobs_done": jobs_done,
+        "jobs_failed": jobs_failed,
+    }

{dcscope-2.27.0 → dcscope-2.28.1}/dcscope/gui/export/e2plot.py

@@ -60,7 +60,7 @@ class ExportPlot(QtWidgets.QDialog):
                                                               'Output Folder')
             if path:
                 for ii, plot in enumerate(self.pipeline.plots):
-                    fn = "SO-plot_{}_{}.{}".format(ii, plot.name, fmt)
+                    fn = f"SO-plot_{ii}_{plot.name}.{fmt}"
                     # remove bad characters from file name
                     fn = get_valid_filename(fn)
                     fnames[plot.identifier] = pathlib.Path(path) / fn