shinestacker 1.6.1__py3-none-any.whl → 1.8.0__py3-none-any.whl

shinestacker/_version.py

@@ -1 +1 @@
-__version__ = '1.6.1'
+__version__ = '1.8.0'

shinestacker/algorithms/corrections.py

@@ -0,0 +1,26 @@
+# pylint: disable=C0114, C0115, C0116, E1101
+import numpy as np
+import cv2
+from ..config.constants import constants
+
+
+def gamma_correction(img, gamma):
+    max_px_val = constants.MAX_UINT8 if img.dtype == np.uint8 else constants.MAX_UINT16
+    ar = np.arange(0, max_px_val + 1, dtype=np.float64)
+    lut = (((ar / max_px_val) ** (1.0 / gamma)) * max_px_val).astype(img.dtype)
+    return cv2.LUT(img, lut) if img.dtype == np.uint8 else np.take(lut, img)
+
+
+def contrast_correction(img, k):
+    max_px_val = constants.MAX_UINT8 if img.dtype == np.uint8 else constants.MAX_UINT16
+    ar = np.arange(0, max_px_val + 1, dtype=np.float64)
+    x = 2.0 * (ar / max_px_val) - 1.0
+    # f(x) = x * exp(k) / (1 + (exp(k) - 1)|x|),  -1 < x < +1
+    # note that: f(f(x, k), -k) = x
+    exp_k = np.exp(k)
+    numerator = x * exp_k
+    denominator = 1 + (exp_k - 1) * np.abs(x)
+    corrected = numerator / denominator
+    corrected = (corrected + 1.0) * 0.5 * max_px_val
+    lut = np.clip(corrected, 0, max_px_val).astype(img.dtype)
+    return cv2.LUT(img, lut) if img.dtype == np.uint8 else np.take(lut, img)

shinestacker/algorithms/stack.py

@@ -65,6 +65,9 @@ class FocusStackBase(TaskBase, ImageSequenceManager):
         if self.exif_path != '':
             self.exif_path = os.path.join(working_path, self.exif_path)
 
+    def end_job(self):
+        ImageSequenceManager.end_job(self)
+
 
 def get_bunches(collection, n_frames, n_overlap):
     bunches = [collection[x:x + n_frames]
@@ -100,6 +103,9 @@ class FocusStackBunch(SequentialTask, FocusStackBase):
     def end(self):
         SequentialTask.end(self)
 
+    def end_job(self):
+        FocusStackBase.end_job(self)
+
     def run_step(self, action_count=-1):
         self.print_message(
             color_str(f"fusing bunch: {action_count + 1}/{self.total_action_counts}",
@@ -126,3 +132,6 @@ class FocusStack(FocusStackBase):
 
     def init(self, job, _working_path=''):
         FocusStackBase.init(self, job, self.working_path)
+
+    def end_job(self):
+        FocusStackBase.end_job(self)

shinestacker/algorithms/stack_framework.py

@@ -46,7 +46,8 @@ class StackJob(Job):
 class ImageSequenceManager:
     def __init__(self, name, input_path='', output_path='', working_path='',
                  plot_path=constants.DEFAULT_PLOTS_PATH,
-                 scratch_output_dir=True, resample=1,
+                 scratch_output_dir=True, delete_output_at_end=False,
+                 resample=1,
                  reverse_order=constants.DEFAULT_FILE_REVERSE_ORDER, **_kwargs):
         self.name = name
         self.working_path = working_path
@@ -56,6 +57,7 @@ class ImageSequenceManager:
         self._resample = resample
         self.reverse_order = reverse_order
         self.scratch_output_dir = scratch_output_dir
+        self.delete_output_at_end = delete_output_at_end
         self.enabled = None
         self.base_message = ''
         self._input_full_path = None
@@ -122,6 +124,24 @@ class ImageSequenceManager:
                                      constants.LOG_COLOR_LEVEL_2))
         self.base_message = color_str(self.name, constants.LOG_COLOR_LEVEL_1, "bold")
 
+    def scratch_outout_folder(self):
+        if self.enabled:
+            output_dir = self.output_full_path()
+            list_dir = os.listdir(output_dir)
+            n_files = len(list_dir)
+            if n_files > 0:
+                for filename in list_dir:
+                    file_path = os.path.join(output_dir, filename)
+                    if os.path.isfile(file_path):
+                        os.remove(file_path)
+            self.print_message(
+                color_str(f"output directory {self.output_path} content erased",
+                          'yellow'))
+        else:
+            self.print_message(
+                color_str(f"module disabled, output directory {self.output_path}"
+                          " not scratched", 'yellow'))
+
     def init(self, job):
         if self.working_path == '':
             self.working_path = job.working_path
@@ -130,22 +150,10 @@ class ImageSequenceManager:
         if not os.path.exists(output_dir):
             os.makedirs(output_dir)
         else:
-            list_dir = os.listdir(output_dir)
-            if len(list_dir) > 0:
+            if len(os.listdir(output_dir)):
                 if self.scratch_output_dir:
-                    if self.enabled:
-                        for filename in list_dir:
-                            file_path = os.path.join(output_dir, filename)
-                            if os.path.isfile(file_path):
-                                os.remove(file_path)
-                        self.print_message(
-                            color_str(f": output directory {self.output_path} content erased",
-                                      'yellow'))
-                    else:
-                        self.print_message(
-                            color_str(f": module disabled, output directory {self.output_path}"
-                                      " not scratched", 'yellow'))
-                else:
+                    self.scratch_outout_folder()
+                elif self.enabled:
                     self.print_message(
                         color_str(
                             f": output directory {self.output_path} not empty, "
@@ -168,6 +176,11 @@ class ImageSequenceManager:
                     self._input_filepaths.append(filepath)
         job.add_action_path(self.output_path)
 
+    def end_job(self):
+        if self.delete_output_at_end:
+            self.scratch_outout_folder()
+            os.rmdir(self.output_full_path())
+
     def folder_list_str(self):
         if isinstance(self.input_full_path(), list):
             file_list = ", ".join(
@@ -206,6 +219,9 @@ class ReferenceFrameTask(SequentialTask, ImageSequenceManager):
     def end(self):
         SequentialTask.end(self)
 
+    def end_job(self):
+        ImageSequenceManager.end_job(self)
+
     def run_frame(self, _idx, _ref_idx):
         return None
 
@@ -323,6 +339,9 @@ class CombinedActions(ReferenceFrameTask):
             if a.enabled:
                 a.end()
 
+    def end_job(self):
+        ReferenceFrameTask.end_job(self)
+
     def sequential_processing(self):
         for a in self._actions:
             if a.sequential_processing():

shinestacker/algorithms/utils.py

@@ -140,8 +140,12 @@ def save_plot(filename, fig=None):
         if not os.path.isdir(dir_path):
             os.makedirs(dir_path)
         if fig is None:
+            logging_level = logging.getLogger().level
+            logger = logging.getLogger()
+            logger.setLevel(logging.WARNING)
             fig = plt.gcf()
-        fig.savefig(filename, dpi=150)
+            fig.savefig(filename, dpi=150)
+            logger.setLevel(logging_level)
         if config.JUPYTER_NOTEBOOK:
             plt.show()
         plt.close(fig)

shinestacker/app/args_parser_opts.py

@@ -1,4 +1,6 @@
 # pylint: disable=C0114, C0116
+import sys
+
 
 def add_project_arguments(parser):
     parser.add_argument('-x', '--expert', action='store_true', help='''
@@ -25,3 +27,40 @@ set side-by-side view.
     view_group.add_argument('-v3', '--view-top-bottom', action='store_true', help='''
 set top-bottom view.
 ''')
+
+
+def extract_positional_filename():
+    positional_filename = None
+    filtered_args = []
+    for arg in sys.argv[1:]:
+        if not arg.startswith('-') and not positional_filename:
+            positional_filename = arg
+        else:
+            filtered_args.append(arg)
+    return positional_filename, filtered_args
+
+
+def setup_filename_argument(parser, use_const=True):
+    if use_const:
+        parser.add_argument('-f', '--filename', nargs='?', const=True, help='''
+filename to open. Can be a project file or image file.
+Multiple files can be specified separated by ';'.
+''')
+    else:
+        parser.add_argument('-f', '--filename', nargs='?', help='''
+filename to open. Can be a project file or image file.
+Multiple files can be specified separated by ';'.
+''')
+
+
+def process_filename_argument(args, positional_filename):
+    filename = args.get('filename')
+    if positional_filename and not filename:
+        filename = positional_filename
+    if filename is True:
+        if positional_filename:
+            filename = positional_filename
+        else:
+            print("Error: -f flag used but no filename provided", file=sys.stderr)
+            sys.exit(1)
+    return filename

shinestacker/app/gui_utils.py

@@ -1,12 +1,15 @@
 # pylint: disable=C0114, C0116, E0611, R0913, R0917
 import os
 import sys
-from PySide6.QtCore import QCoreApplication, QProcess
-from PySide6.QtGui import QAction
+import logging
+from PySide6.QtCore import Qt, QCoreApplication, QProcess
+from PySide6.QtGui import QAction, QIcon
 from shinestacker.config.constants import constants
 from shinestacker.config.config import config
+from shinestacker.config.settings import StdPathFile
 from shinestacker.app.about_dialog import show_about_dialog
 from shinestacker.app.settings_dialog import show_settings_dialog
+from shinestacker.core.logging import setup_logging
 
 
 def disable_macos_special_menu_items():
@@ -71,3 +74,17 @@ def set_css_style(app):
         }
 """
     app.setStyleSheet(css_style)
+
+
+def make_app(application_class):
+    setup_logging(console_level=logging.DEBUG, file_level=logging.DEBUG, disable_console=True,
+                  log_file=StdPathFile('shinestacker.log').get_file_path())
+    app = application_class(sys.argv)
+    if config.DONT_USE_NATIVE_MENU:
+        app.setAttribute(Qt.AA_DontUseNativeMenuBar)
+    else:
+        disable_macos_special_menu_items()
+    icon_path = f"{os.path.dirname(__file__)}/../gui/ico/shinestacker.png"
+    app.setWindowIcon(QIcon(icon_path))
+    set_css_style(app)
+    return app

shinestacker/app/main.py

@@ -1,27 +1,26 @@
 # pylint: disable=C0114, C0115, C0116, C0413, E0611, R0903, E1121, W0201, R0915, R0912
 import sys
-import os
-import logging
 import argparse
 import matplotlib
 import matplotlib.backends.backend_pdf
 matplotlib.use('agg')
 from PySide6.QtWidgets import (QApplication, QMainWindow, QVBoxLayout, QHBoxLayout, QStackedWidget,
                                QMenu, QMessageBox, QDialog, QLabel, QListWidget, QPushButton)
-from PySide6.QtGui import QAction, QIcon, QGuiApplication
-from PySide6.QtCore import Qt, QEvent, QTimer, Signal
+from PySide6.QtGui import QAction, QGuiApplication
+from PySide6.QtCore import QEvent, QTimer, Signal
 from shinestacker.config.config import config
 config.init(DISABLE_TQDM=True, COMBINED_APP=True, DONT_USE_NATIVE_MENU=True)
 from shinestacker.config.constants import constants
-from shinestacker.config.settings import StdPathFile
-from shinestacker.core.logging import setup_logging
 from shinestacker.gui.main_window import MainWindow
 from shinestacker.retouch.image_editor_ui import ImageEditorUI
-from shinestacker.app.gui_utils import (
-    disable_macos_special_menu_items, fill_app_menu, set_css_style)
+from shinestacker.app.gui_utils import fill_app_menu
 from shinestacker.app.help_menu import add_help_action
 from shinestacker.app.open_frames import open_frames
-from shinestacker.app.args_parser_opts import add_project_arguments, add_retouch_arguments
+from shinestacker.app.args_parser_opts import (
+    add_project_arguments, add_retouch_arguments, extract_positional_filename,
+    setup_filename_argument, process_filename_argument
+)
+from shinestacker.app.gui_utils import make_app
 
 
 class SelectionDialog(QDialog):
@@ -206,15 +205,12 @@ class Application(QApplication):
 
 
 def main():
+    positional_filename, filtered_args = extract_positional_filename()
     parser = argparse.ArgumentParser(
-        prog=f'{constants.APP_STRING.lower()}-retouch',
+        prog=f'{constants.APP_STRING.lower()}',
         description='Focus stacking App.',
         epilog=f'This app is part of the {constants.APP_STRING} package.')
-    parser.add_argument('-f', '--filename', nargs='?', help='''
-if a single file is specified, it can be either a project or an image.
-Multiple frames can be specified as a list of files.
-Multiple files can be specified separated by ';'.
-''')
+    setup_filename_argument(parser, use_const=True)
     app_group = parser.add_mutually_exclusive_group()
     app_group.add_argument('-j', '--project', action='store_true', help='''
 open project window at startup instead of project windows (default).
@@ -224,24 +220,17 @@ open retouch window at startup instead of project windows.
 ''')
     add_project_arguments(parser)
     add_retouch_arguments(parser)
-    args = vars(parser.parse_args(sys.argv[1:]))
-    filename = args['filename']
+    args = vars(parser.parse_args(filtered_args))
+    filename = process_filename_argument(args, positional_filename)
     path = args['path']
     if filename and path:
         print("can't specify both arguments --filename and --path", file=sys.stderr)
         sys.exit(1)
-    setup_logging(console_level=logging.DEBUG, file_level=logging.DEBUG, disable_console=True,
-                  log_file=StdPathFile('shinestacker.log').get_file_path())
-    app = Application(sys.argv)
-    if config.DONT_USE_NATIVE_MENU:
-        app.setAttribute(Qt.AA_DontUseNativeMenuBar)
-    else:
-        disable_macos_special_menu_items()
-    icon_path = f"{os.path.dirname(__file__)}/../gui/ico/shinestacker.png"
-    app.setWindowIcon(QIcon(icon_path))
+
+    app = make_app(Application)
     main_app = MainApp()
     app.main_app = main_app
-    set_css_style(app)
+
     main_app.show()
     main_app.activateWindow()
     if args['expert']:

shinestacker/app/project.py

@@ -1,24 +1,23 @@
 # pylint: disable=C0114, C0115, C0116, C0413, E0611, R0903, E1121, W0201
 import os
 import sys
-import logging
 import argparse
 import matplotlib
 import matplotlib.backends.backend_pdf
 matplotlib.use('agg')
 from PySide6.QtWidgets import QApplication, QMenu
-from PySide6.QtGui import QIcon
-from PySide6.QtCore import Qt, QTimer, QEvent
+from PySide6.QtCore import QTimer, QEvent
 from shinestacker.config.config import config
 config.init(DISABLE_TQDM=True, DONT_USE_NATIVE_MENU=True)
 from shinestacker.config.constants import constants
-from shinestacker.config.settings import StdPathFile
-from shinestacker.core.logging import setup_logging
 from shinestacker.gui.main_window import MainWindow
-from shinestacker.app.gui_utils import (
-    disable_macos_special_menu_items, fill_app_menu, set_css_style)
+from shinestacker.app.gui_utils import fill_app_menu
 from shinestacker.app.help_menu import add_help_action
-from shinestacker.app.args_parser_opts import add_project_arguments
+from shinestacker.app.args_parser_opts import (
+    add_project_arguments, extract_positional_filename,
+    setup_filename_argument, process_filename_argument
+)
+from shinestacker.app.gui_utils import make_app
 
 
 class ProjectApp(MainWindow):
@@ -49,31 +48,21 @@ class Application(QApplication):
 
 
 def main():
+    positional_filename, filtered_args = extract_positional_filename()
     parser = argparse.ArgumentParser(
         prog=f'{constants.APP_STRING.lower()}-project',
         description='Manage and run focus stack jobs.',
         epilog=f'This app is part of the {constants.APP_STRING} package.')
-    parser.add_argument('-f', '--filename', nargs='?', help='''
-project filename.
-''')
+    setup_filename_argument(parser, use_const=True)
     add_project_arguments(parser)
-    args = vars(parser.parse_args(sys.argv[1:]))
-    setup_logging(console_level=logging.DEBUG, file_level=logging.DEBUG, disable_console=True,
-                  log_file=StdPathFile('shinestacker.log').get_file_path())
-    app = Application(sys.argv)
-    if config.DONT_USE_NATIVE_MENU:
-        app.setAttribute(Qt.AA_DontUseNativeMenuBar)
-    else:
-        disable_macos_special_menu_items()
-    icon_path = f"{os.path.dirname(__file__)}/../gui/ico/shinestacker.png"
-    app.setWindowIcon(QIcon(icon_path))
-    set_css_style(app)
+    args = vars(parser.parse_args(filtered_args))
+    filename = process_filename_argument(args, positional_filename)
+    app = make_app(Application)
     window = ProjectApp()
     if args['expert']:
         window.set_expert_options()
     app.window = window
     window.show()
-    filename = args['filename']
     if filename:
         QTimer.singleShot(100, lambda: window.project_controller.open_project(filename))
     elif args['new-project']:

shinestacker/app/retouch.py

@@ -1,22 +1,20 @@
 # pylint: disable=C0114, C0115, C0116, C0413, E0611, R0903, E1121, W0201
-import os
 import sys
-import logging
 import argparse
 from PySide6.QtWidgets import QApplication, QMenu
-from PySide6.QtGui import QIcon
-from PySide6.QtCore import Qt, QEvent
+from PySide6.QtCore import QEvent
 from shinestacker.config.config import config
 config.init(DISABLE_TQDM=True, DONT_USE_NATIVE_MENU=True)
 from shinestacker.config.constants import constants
-from shinestacker.config.settings import StdPathFile
-from shinestacker.core.logging import setup_logging
 from shinestacker.retouch.image_editor_ui import ImageEditorUI
-from shinestacker.app.gui_utils import (
-    disable_macos_special_menu_items, fill_app_menu, set_css_style)
+from shinestacker.app.gui_utils import fill_app_menu
 from shinestacker.app.help_menu import add_help_action
 from shinestacker.app.open_frames import open_frames
-from shinestacker.app.args_parser_opts import add_retouch_arguments
+from shinestacker.app.args_parser_opts import (
+    add_retouch_arguments, extract_positional_filename,
+    setup_filename_argument, process_filename_argument
+)
+from shinestacker.app.gui_utils import make_app
 
 
 class RetouchApp(ImageEditorUI):
@@ -42,31 +40,20 @@ class Application(QApplication):
 
 
 def main():
+    positional_filename, filtered_args = extract_positional_filename()
     parser = argparse.ArgumentParser(
         prog=f'{constants.APP_STRING.lower()}-retouch',
         description='Final retouch focus stack image from individual frames.',
         epilog=f'This app is part of the {constants.APP_STRING} package.')
-    parser.add_argument('-f', '--filename', nargs='?', help='''
-import frames from files.
-Multiple files can be specified separated by ';'.
-''')
+    setup_filename_argument(parser, use_const=True)
     add_retouch_arguments(parser)
-    args = vars(parser.parse_args(sys.argv[1:]))
-    filename = args['filename']
+    args = vars(parser.parse_args(filtered_args))
+    filename = process_filename_argument(args, positional_filename)
     path = args['path']
     if filename and path:
         print("can't specify both arguments --filename and --path", file=sys.stderr)
         sys.exit(1)
-    setup_logging(console_level=logging.DEBUG, file_level=logging.DEBUG, disable_console=True,
-                  log_file=StdPathFile('shinestacker.log').get_file_path())
-    app = Application(sys.argv)
-    if config.DONT_USE_NATIVE_MENU:
-        app.setAttribute(Qt.AA_DontUseNativeMenuBar)
-    else:
-        disable_macos_special_menu_items()
-    icon_path = f"{os.path.dirname(__file__)}/../gui/ico/shinestacker.png"
-    app.setWindowIcon(QIcon(icon_path))
-    set_css_style(app)
+    app = make_app(Application)
     editor = RetouchApp()
     app.editor = editor
     editor.show()

shinestacker/app/settings_dialog.py

@@ -1,23 +1,28 @@
 # pylint: disable=C0114, C0115, C0116, E0611, W0718, R0903, E0611, R0902
 from PySide6.QtCore import Signal
 from PySide6.QtWidgets import QFrame, QLabel, QCheckBox, QComboBox, QDoubleSpinBox, QSpinBox
-from .. gui.config_dialog import ConfigDialog
 from .. config.settings import Settings
 from .. config.constants import constants
 from .. config.gui_constants import gui_constants
+from .. gui.config_dialog import ConfigDialog
+from .. gui.action_config_dialog import AlignFramesConfigBase
 
 
-class SettingsDialog(ConfigDialog):
+class SettingsDialog(ConfigDialog, AlignFramesConfigBase):
     update_project_config_requested = Signal()
     update_retouch_config_requested = Signal()
 
     def __init__(self, parent=None, project_settings=True, retouch_settings=True):
+        AlignFramesConfigBase.__init__(self)
         self.project_settings = project_settings
         self.retouch_settings = retouch_settings
         self.settings = Settings.instance()
         self.expert_options = None
         self.combined_actions_max_threads = None
         self.align_frames_max_threads = None
+        self.detector = None
+        self.descriptor = None
+        self.matching_method = None
         self.focus_stack_max_threads = None
         self.view_strategy = None
         self.min_mouse_step_brush_fraction = None
@@ -58,6 +63,32 @@ class SettingsDialog(ConfigDialog):
         self.container_layout.addRow("Max num. of cores, align frames:",
                                      self.align_frames_max_threads)
 
+        def change_match_config():
+            self.change_match_config(
+                self.detector, self.descriptor,
+                self. matching_method, self.show_info)
+
+        self.detector = QComboBox()
+        self.detector.addItems(constants.VALID_DETECTORS)
+        self.descriptor = QComboBox()
+        self.descriptor.addItems(constants.VALID_DESCRIPTORS)
+        self.matching_method = QComboBox()
+        self.info_label = QLabel()
+        self.info_label.setStyleSheet("color: orange; font-style: italic;")
+        self.matching_method = QComboBox()
+        for k, v in zip(self.MATCHING_METHOD_OPTIONS, constants.VALID_MATCHING_METHODS):
+            self.matching_method.addItem(k, v)
+        self.detector.setToolTip(self.DETECTOR_DESCRIPTOR_TOOLTIPS['detector'])
+        self.descriptor.setToolTip(self.DETECTOR_DESCRIPTOR_TOOLTIPS['descriptor'])
+        self.matching_method.setToolTip(self.DETECTOR_DESCRIPTOR_TOOLTIPS['match_method'])
+        self.detector.currentIndexChanged.connect(change_match_config)
+        self.descriptor.currentIndexChanged.connect(change_match_config)
+        self.matching_method.currentIndexChanged.connect(change_match_config)
+        self.container_layout.addRow('Detector:', self.detector)
+        self.container_layout.addRow('Descriptor:', self.descriptor)
+        self.container_layout.addRow(self.info_label)
+        self.container_layout.addRow('Match method:', self.matching_method)
+
         self.focus_stack_max_threads = QSpinBox()
         self.focus_stack_max_threads.setRange(0, 64)
         self.focus_stack_max_threads.setValue(
@@ -115,7 +146,14 @@ class SettingsDialog(ConfigDialog):
                 })
             self.settings.set(
                 'align_frames_params', {
-                    'max_threads': self.align_frames_max_threads.value()
+                    'max_threads':
+                        self.align_frames_max_threads.value(),
+                    'detector':
+                        self.descriptor.currentText(),
+                    'descriptor':
+                        self.descriptor.currentText(),
+                    'match_method':
+                        self.matching_method.itemData(self.matching_method.currentIndex())
                 })
             self.settings.set(
                 'focus_stack_params', {
@@ -148,6 +186,11 @@ class SettingsDialog(ConfigDialog):
             self.expert_options.setChecked(constants.DEFAULT_EXPERT_OPTIONS)
             self.combined_actions_max_threads.setValue(constants.DEFAULT_MAX_FWK_THREADS)
             self.align_frames_max_threads.setValue(constants.DEFAULT_ALIGN_MAX_THREADS)
+            self.detector.setCurrentText(constants.DEFAULT_DETECTOR)
+            self.descriptor.setCurrentText(constants.DEFAULT_DESCRIPTOR)
+            idx = self.matching_method.findData(constants.DEFAULT_MATCHING_METHOD)
+            if idx >= 0:
+                self.matching_method.setCurrentIndex(idx)
             self.focus_stack_max_threads.setValue(constants.DEFAULT_PY_MAX_THREADS)
         if self.retouch_settings:
             idx = self.view_strategy.findData(constants.DEFAULT_VIEW_STRATEGY)

shinestacker/config/settings.py

@@ -42,7 +42,10 @@ DEFAULT_SETTINGS = {
         'max_threads': constants.DEFAULT_MAX_FWK_THREADS
     },
     'align_frames_params': {
-        'max_threads': constants.DEFAULT_ALIGN_MAX_THREADS
+        'max_threads': constants.DEFAULT_ALIGN_MAX_THREADS,
+        'detector': constants.DEFAULT_DETECTOR,
+        'descriptor': constants.DEFAULT_DESCRIPTOR,
+        'match_method': constants.DEFAULT_MATCHING_METHOD
     },
     'focus_stack_params': {
         'max_threads': constants.DEFAULT_PY_MAX_THREADS

shinestacker/core/core_utils.py

@@ -28,8 +28,7 @@ def make_tqdm_bar(name, size, ncols=80):
 def get_app_base_path():
     if getattr(sys, 'frozen', False):
         return os.path.dirname(os.path.abspath(sys.executable))
-    else:
-        return os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+    return os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
 
 def running_under_windows() -> bool:
@@ -53,4 +52,5 @@ def setup_matplotlib_mode():
         __IPYTHON__ # noqa
     except Exception:
         matplotlib.use('agg')
+    matplotlib.pyplot.set_loglevel("warning")
     matplotlib.rcParams['pdf.fonttype'] = 42

shinestacker/core/framework.py

@@ -146,6 +146,9 @@ class TaskBase:
     def sub_message_r(self, msg='', level=logging.INFO):
         self.sub_message(msg, level, self.end_r, self.begin_r, False)
 
+    def end_job(self):
+        pass
+
 
 class Job(TaskBase):
     def __init__(self, name, logger_name=None, log_file='', callbacks=None, **kwargs):
@@ -188,6 +191,8 @@ class Job(TaskBase):
                                  self.id, self.name) is False:
                     raise RunStopException(self.name)
                 a.run()
+        for a in self.__actions:
+            a.end_job()
 
 
 class SequentialTask(TaskBase):
@@ -261,11 +266,11 @@ class SequentialTask(TaskBase):
                 try:
                     result = future.result()
                     if result:
-                        self.print_message(color_str(
+                        self.print_message_r(color_str(
                             f"completed processing step: {self.idx_tot_str(idx)}",
                             constants.LOG_COLOR_LEVEL_1))
                     else:
-                        self.print_message(color_str(
+                        self.print_message_r(color_str(
                             f"failed processing step: {self.idx_tot_str(idx)}",
                             constants.LOG_COLOR_WARNING))
                     self.current_action_count += 1

shinestacker/core/logging.py

@@ -64,9 +64,9 @@ def setup_logging(console_level=logging.INFO, file_level=logging.DEBUG, log_file
     if log_file is not None:
         if log_file == '':
             today = datetime.date.today().strftime("%Y-%m-%d")
-            log_file = f"logs/{constants.APP_STRING.lower()}-{today}.log"
+            log_file = os.path.join('logs', f"{constants.APP_STRING.lower()}-{today}.log")
         if not os.path.isabs(log_file):
-            log_file = os.path.join(get_app_base_path(), {log_file})
+            log_file = os.path.join(get_app_base_path(), log_file)
         Path(log_file).parent.mkdir(parents=True, exist_ok=True)
         file_handler = logging.FileHandler(log_file)
         file_handler.setLevel(file_level)