batoolset 0.1.0__tar.gz

batoolset-0.1.0/LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2024, baigouy
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

batoolset-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: batoolset
+Version: 0.1.0
+Summary: An aggregate of functions I find useful
+Home-page: https://github.com/baigouy/batoolset
+Author: Benoit Aigouy
+Author-email: benoit.aigouy@gmail.com
+License: BSD
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7, <3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: czifile
+Requires-Dist: Markdown
+Requires-Dist: matplotlib>=3.5.2
+Requires-Dist: numpy
+Requires-Dist: Pillow>=8.1.2
+Requires-Dist: PyQt6
+Requires-Dist: read-lif
+Requires-Dist: scikit-image>=0.19.3
+Requires-Dist: scipy>=1.7.3
+Requires-Dist: scikit-learn>=1.0.2
+Requires-Dist: tifffile>=2021.11.2
+Requires-Dist: tqdm
+Requires-Dist: natsort
+Requires-Dist: numexpr
+Requires-Dist: urllib3
+Requires-Dist: qtawesome
+Requires-Dist: pandas
+Requires-Dist: numba
+Requires-Dist: elasticdeform
+Requires-Dist: roifile
+Requires-Dist: prettytable
+Requires-Dist: pyperclip
+Requires-Dist: QtPy>=2.1.0
+Requires-Dist: Deprecated
+Requires-Dist: Requests
+Requires-Dist: python-bioformats
+Requires-Dist: python-javabridge
+Requires-Dist: pyautogui
+
+# batoolset
+An aggregate of functions I find useful

batoolset-0.1.0/README.md

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+# batoolset
+An aggregate of functions I find useful

batoolset-0.1.0/batoolset/GUI/list_gui.py

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+# support list for writing or not stuff
+import os
+from batoolset.settings.global_settings import set_UI # set the UI to qtpy
+set_UI()
+from qtpy import QtCore, QtWidgets
+from qtpy.QtCore import Qt,Signal
+from qtpy.QtWidgets import QWidget, QAbstractItemView, QListWidget, QVBoxLayout, QListWidgetItem, QToolBar, \
+    QToolButton, \
+    QLabel, QAction
+import pyperclip as clip
+from batoolset.dialogs.opensave import saveFileDialog
+from batoolset.utils.loadlist import loadlist, save_list_to_file
+import os
+import platform
+import subprocess
+from batoolset.files.tools import smart_name_parser
+import qtawesome as qta
+from natsort import natsorted
+from batoolset.tools.logger import TA_logger
+logger = TA_logger()
+
+
+__DEBUG__ = True
+
+IMAGES_2D = ['.tif', '.tiff', '.jpg', '.jpeg', '.png', '.tga', '.bmp']
+STACKS = ['.tif', '.tiff', '.lif', '.czi', '.lif', '.lsm']
+LISTS = ['.lst', '.txt']
+FASTA = ['.fa','.fna','.fasta']
+PYTA_DEFAULT = IMAGES_2D + LISTS
+
+class CustomListWidget(QListWidget):
+    orderChanged = Signal()
+
+    def dropEvent(self, event):
+        super().dropEvent(event)
+        self.orderChanged.emit()
+
+class ListGUI(QWidget):
+    orderChanged = Signal()
+    deletePressed = Signal() # can be used in parent to detect that this was called allowing some action to be taken (more elegant than the callback or the method overlaod in several aspects)!
+    # TODO define supported formats --> TODO
+    def __init__(self, parent=None, file_to_load=None, supported_files=None, custom_label='Please Drag and Drop files below:', default_double_click_behaviour='full_no_ext', enable_folder_DND=True, detect_list_order_change=False):
+        super().__init__(parent)
+        if detect_list_order_change:
+            self.list = CustomListWidget(self)  # a list that contains files to read or play with
+        #     self.list.orderChanged.connect(self.check_order_changed)
+        else:
+            self.list = QListWidget(self)
+        self.list.setSelectionMode(QAbstractItemView.ExtendedSelection)
+        # self.list.selectionModel().selectionChanged.connect(self.selectionChanged)  # connect it to sel change
+
+        # self.list.selectionModel().selectionChanged.connect(self.listSelectionChanged)
+
+        self.list.itemDoubleClicked.connect(self.open_corresponding_folder)
+
+        self.enable_folder_DND = enable_folder_DND
+        self.default_double_click_behaviour = default_double_click_behaviour
+
+        layout = QVBoxLayout()
+        lab = QLabel(custom_label)
+        layout.addWidget(lab)
+        layout.addWidget(self.list)
+
+        self.setLayout(layout)
+        # allow support of DND
+        self.setAcceptDrops(True)
+        self.supported_files = supported_files
+
+        # status_bar = QStatusBar()
+        # layout.addWidget(status_bar)
+        # self.list_commands(**kwargs)
+        self.list_commands()
+
+        if file_to_load is not None:
+            self.load_list(file_to_load)
+            # if __DEBUG__:
+            # fake sel list
+            # pass
+
+        # allow move objects within the list
+        self.list.setDragDropMode(QAbstractItemView.InternalMove)  # j'adore --> maybe put this as an option
+
+        # allows sorting of lists
+        # self.list.setSortingEnabled(True) # we don't want list to be sorted by default
+        # self.list.sortItems()  # ascending by default
+        self.list.sortItems(QtCore.Qt.DescendingOrder)  # todo MAKE it a sort button
+
+        # both lines below support objects handling directly from the list --> a gain of time
+        self.list.itemChanged.connect(self.item_changed)
+        self._object_dict = {} # dirty hack to store objects and allow for DND of objects
+
+    def item_changed(self, item):
+        obj = self._object_dict.get(str(item))  # Get the object from the dictionary
+        if obj is not None:
+            # Do something with the object
+            print("Object changed:", obj)
+    def check_order_changed(self):
+        # Implement your order changed logic here
+        print("Order changed!")
+        # self.setWindowTitle('test')
+
+    def open_corresponding_folder(self, double_clicked_item):
+        try:
+            self.open_folder(smart_name_parser(double_clicked_item.toolTip(), ordered_output=[self.default_double_click_behaviour])[0]) #'full_no_ext'
+        except:
+            # no big deal if it fails
+            pass
+
+    def open_folder(self, path):
+        if platform.system() == 'Darwin':
+            subprocess.Popen(['open', path])
+        elif platform.system() == 'Windows':
+            os.startfile(path)
+        elif platform.system() == 'Linux':
+            subprocess.Popen(["xdg-open", path])
+
+    def list_commands(self): #,**kwargs):
+
+        # buttons_to_hide = []
+        # if 'buttons_to_remove' in kwargs:
+        #     buttons_to_hide = kwargs['buttons_to_remove']
+        #     if isinstance(buttons_to_hide, str):
+        #         buttons_to_hide = [buttons_to_hide]
+
+        # self.penSize = QSpinBox(objectName='penSize')
+        # self.penSize.setSingleStep(1)
+        # self.penSize.setRange(1, 256)
+        # self.penSize.setValue(3)
+        # self.penSize.valueChanged.connect(self.penSizechange)
+
+        # self.channels = QComboBox(objectName='channels')
+        # self.channels.addItem("merge")
+        # self.channels.addItem("0")
+        # self.channels.addItems(["1", "2", "3"])
+        # self.channels.currentIndexChanged.connect(self.channelChange)
+
+        self.tb = QToolBar()
+        #
+        toolButton = QToolButton()
+        # toolButton.setText('Draw')
+
+
+        save_action = QAction(qta.icon('fa5.save'), 'Save image list', self)
+        save_action.triggered.connect(self.save_list)
+        # END KEEP
+        toolButton.setDefaultAction(save_action)
+        self.tb.addWidget(toolButton)
+        #
+        # toolButton2 = QToolButton()
+        # toolButton2.setText('Draw')
+        # toolButton2.setIcon(self.style().standardIcon(QStyle.SP_DialogApplyButton))
+        # tb.addWidget(toolButton2)
+        #
+        # toolButton3 = QToolButton()
+        # toolButton3.setText('Draw')
+        # toolButton3.setIcon(self.style().standardIcon(QStyle.SP_DialogCancelButton))
+        # tb.addWidget(toolButton3)
+        #
+        # toolButton4 = QToolButton()
+        # toolButton4.setText('Draw')
+        # toolButton4.setIcon(self.style().standardIcon(QStyle.SP_DialogCloseButton))
+        # tb.addWidget(toolButton4)
+
+        toolButton5 = QToolButton()
+        # toolButton5.setText("Delete")
+        # toolButton5.setIcon(self.style().standardIcon(QStyle.SP_TrashIcon))
+        # toolButton5.addAction(dqsdqsdq)
+        # pkoi marche pas
+        # KEEP
+
+        delete_sel_action = QAction(qta.icon('mdi.delete-outline'), 'Delete selection', self)
+        # toolButton5.addAction(delete_sel_action) # this stuff adds a dropwdon that can be opened by pressing a long time on the button --> keep in mind cause can be useful
+        delete_sel_action.triggered.connect(self.removeSel)
+        # END KEEP
+        toolButton5.setDefaultAction(delete_sel_action)
+        self.tb.addWidget(toolButton5)
+
+        toolButton6 = QToolButton()
+        # toolButton6.setText("Copy")
+        # toolButton6.setIcon(qta.icon('fa5.copy'))
+        copy_action = QAction(qta.icon('fa5.copy'), 'Copy selection to the system clipboard', self)
+        copy_action.triggered.connect(self.sel_to_clipboard)
+        toolButton6.setDefaultAction(copy_action)
+        # toolButton6.ad#dAction(print('toto'))
+        self.tb.addWidget(toolButton6)
+
+        toolButton7 = QToolButton()
+        # toolButton7.setText("Paste")
+        # toolButton7.setIcon(qta.icon('fa.paste'))
+        paste_action = QAction(qta.icon('fa.paste'), 'Paste the system clipboard to the list', self)
+        paste_action.triggered.connect(self.paste_from_clipboard)
+        toolButton7.setDefaultAction(paste_action)
+        self.tb.addWidget(toolButton7)
+
+        toolButton8 = QToolButton()
+        sort_action = QAction(qta.icon('mdi.sort-alphabetical-ascending'), 'Sort list (using the Natsort algorithm)', self)
+        sort_action.triggered.connect(self.natsort_list)
+        toolButton8.setDefaultAction(sort_action)
+        self.tb.addWidget(toolButton8)
+
+        # tb.addWidget(self.channels)
+
+        # tb.addAction("Save")
+        # tb.addAction("sq...")
+        # tb.addWidget(self.penSize)
+
+        # could have show and hide mask here --> see how I can do that --> but do not delete it in fact
+
+        self.layout().addWidget(self.tb)
+
+    # disable item internal move and list addition, just selection is kept
+    def freeze(self, bool):
+        self.tb.setEnabled(not bool)
+        # TODO disable DND of list component
+        # if bool:
+        # self.list.setDragDropMode(QAbstractItemView.InternalMove)
+        # self.setAcceptDrops(True)
+        # else:
+        # self.list.setDragDropMode(QAbstractItemView.InternalMove)
+        self.setAcceptDrops(not bool)
+        # how to disable item reorder
+        # QGraphicsItem.ItemIsMovable
+        # we also prevent internal drag --> it's a way to keep the list functional
+
+
+
+        # ça ne marche pas
+        # print(bool)
+        if bool:
+
+            # print('entering o,ne')
+
+            # disable item internal move
+            for iii in range(self.list.count()):
+                item = self.list.item(iii)
+
+                # is there a bug here
+                if  item.flags() & Qt.ItemIsDragEnabled:
+                    item.setFlags(item.flags() ^ Qt.ItemIsDragEnabled)
+                # item.setFlags(item.flags() ^ Qt.ItemIsDropEnabled)
+
+                # if iii == 0:
+                #     if item.flags() & Qt.ItemIsDragEnabled:
+                #         print( "ItemIsDragEnabled", item)
+                #     else:
+                #         print("not ItemIsDragEnabled", item)
+
+        else:
+            # allow item internal move
+            # print('entering two')
+            for iii in range(self.list.count()):
+                item = self.list.item(iii)
+                item.setFlags(item.flags() | Qt.ItemIsDragEnabled)
+                # item.setFlags(item.flags() | Qt.ItemIsDropEnabled)
+                # if iii == 0:
+                #     if item.flags() & Qt.ItemIsDragEnabled:
+                #         print("ItemIsDragEnabled", item)
+                #     else:
+                #         print("not ItemIsDragEnabled", item)
+
+
+    def load_list(self, file_to_load):
+        files = loadlist(file_to_load)
+        if files is not None:
+            # populate the list
+            for file in files:
+                self.add_file_to_list_if_supported(file)
+        else:
+            print('list could not be loaded/invalid list --> sorry')
+
+    # def selectionChanged(self):
+    #     print('selection changed to override')
+
+    # allow DND
+    def dragEnterEvent(self, event):
+        if not self.acceptDrops():
+            logger.warning('Drag and drop not supported in "Preview" mode, please select another tab.')
+            event.ignore()
+            return
+        if event.mimeData().hasUrls():
+            event.accept()
+        else:
+            event.ignore()
+
+    def dragMoveEvent(self, event):
+        if not self.acceptDrops():
+            logger.warning('Drag and drop not supported in "Preview" mode, please select another tab.')
+            event.ignore()
+            return
+        if event.mimeData().hasUrls():
+            event.setDropAction(QtCore.Qt.CopyAction)
+            event.accept()
+        else:
+            event.ignore()
+
+    # handle DND on drop
+    def dropEvent(self, event):
+        super().dropEvent(event)
+        self.orderChanged.emit()
+
+        if not self.acceptDrops():
+            logger.warning('Drag and drop not supported in "Preview" mode, please select another tab.')
+            event.ignore()
+            return
+
+        if event.mimeData().hasUrls():
+            event.setDropAction(QtCore.Qt.CopyAction)
+            event.accept()
+            urls = []
+            for url in event.mimeData().urls():
+                urls.append(url.toLocalFile())
+            # add all dropped items to the list
+            for url in urls:
+                # item = QListWidgetItem(os.path.basename(url), self.list)
+                # item.setToolTip(url)
+                # self.list.addItem(item)
+                self.add_file_to_list_if_supported(url)
+        else:
+            event.ignore()
+
+    def is_file_supported(self, file):
+        if self.supported_files is None:
+            # accept all by default
+            return True
+        if smart_name_parser(file, ordered_output=['ext'])[0].lower() in self.supported_files:
+            return True
+        return False
+
+    def add_file_to_list_no_check(self, file):
+        item = QListWidgetItem(os.path.basename(file), self.list)
+        item.setToolTip(file)
+        self.list.addItem(item)
+
+    def add_object_to_list_no_check(self, obj): #added this to add non file objects to the list
+        item = QListWidgetItem(str(obj), self.list)
+        item.setToolTip(str(obj))
+        # item.setData(Qt.UserRole, obj)
+        # item.setData(Qt.UserRole, str(obj))
+        self._object_dict[str(item)] = obj  # Store a reference to the object in the dictionary
+        self.list.addItem(item)
+
+    def add_to_list(self, files, check_if_supported=True):
+        if isinstance(files, str):
+            if check_if_supported:
+                self.add_file_to_list_if_supported(files)
+            else:
+                self.add_file_to_list_no_check(files)
+        elif isinstance(files, list):
+            for file in files:
+                if check_if_supported:
+                    self.add_file_to_list_if_supported(file)
+                else:
+                    self.add_file_to_list_no_check(file)
+        else:
+            print('Non supported, cannot be added to list', files)
+
+    def list_files_in_directory(self, directory_path):
+        files = [os.path.join(directory_path,f) for f in os.listdir(directory_path) if os.path.isfile(os.path.join(directory_path, f))]
+        # print(files)
+        return files
+
+    def add_file_to_list_if_supported(self, file):
+        # print('checking if supported', file)
+        if self.is_file_supported(file) and os.path.isfile(file):
+            ext = smart_name_parser(file, ordered_output=['ext'])[0].lower()
+            if ext in LISTS:
+                TA_list_of_files = loadlist(file)
+                return self.add_to_list(TA_list_of_files, check_if_supported=True)
+            else:
+                self.add_file_to_list_no_check(file)
+        elif self.enable_folder_DND and os.path.isdir(file):
+            files = self.list_files_in_directory(file)
+            for file in files:
+                self.add_file_to_list_if_supported(file)
+
+
+    def get_full_list(self):
+        # return the complete list of files
+        selected_items = []
+        for i in range(self.list.count()):
+            if str(self.list.item(i)) in self._object_dict:
+                selected_items.append(self._object_dict[str(self.list.item(i))])
+            else:
+                selected_items.append(self.list.item(i).toolTip())
+        return selected_items
+
+    def get_selection(self, mode='single'):
+        selected_items = self.list.selectedItems()
+        if selected_items:
+            if mode == 'single':
+                if str(selected_items[0]) in self._object_dict:
+                    return self._object_dict[str(selected_items[0])]
+                # if selected_items[0].data(Qt.UserRole):
+                #     return selected_items[0].data(Qt.UserRole)
+                return selected_items[0].toolTip()
+            else:
+                sel = []
+                for selec in selected_items:
+                    if str(selec) in self._object_dict:
+                        sel.append(self._object_dict[str(selec)])
+                    # elif selec.data(Qt.UserRole):
+                    #     sel.append(selec.data(Qt.UserRole))
+                    else:
+                        sel.append(selec.toolTip())
+                return sel
+        else:
+            return None
+
+    def get_selection_index(self, mode='single'):
+        try:
+            # selected_items = self.list.selectedIndexes() # this is a weird model index object that is largely useless
+            selected_items = [s.row() for s in self.list.selectedIndexes()]
+            # print('selected_items',selected_items)
+            if selected_items:
+                if mode == 'single':
+                    # print('sel', selected_items[0])
+                    return selected_items[0]
+                else:
+                    # sel = []
+                    # for selec in selected_items:
+                    #     sel.append(selec.toolTip())
+                    return selected_items
+            # else:
+        except:
+            pass
+        return None
+
+    def save_list(self):
+        # on va sauver la liste ici
+        lst = self.get_full_list()
+        if lst:
+            path = smart_name_parser(lst[0], ordered_output='parent')
+            path = os.path.join(path, 'list.lst')
+
+            output_file = saveFileDialog(parent_window=self, path=path,
+                                         extensions="Lists (*.lst);;Supported Files (*.lst *.txt);;All Files (*)",
+                                         default_ext='.lst')
+            if output_file is not None:
+                # now do save the list in the folder of the parent of the first file
+                save_list_to_file(lst, output_file)
+                # print(lst, output_file)
+
+    def removeSel(self):
+        selected_items = self.list.selectedItems()
+        self.list.clearSelection()  # Clear selection # required to prevent selection from changing and the software to want to update display or anything alike
+        if not selected_items:
+            self.clearList()
+            self.deletePressed.emit() # send the delete action to the parent
+            return
+
+        # Remove selected items from the list
+        for item in selected_items:
+            # Remove the item from the dictionary
+            if str(item) in self._object_dict:
+                del self._object_dict[str(item)]
+        for item in selected_items:
+            # print('looping')
+            self.list.takeItem(self.list.row(item))
+        self.deletePressed.emit() # send the delete action to the parent
+
+    # faire une copie dans le clip de la selection
+    def sel_to_clipboard(self):
+        sel = self.get_selection(mode='all')
+        if sel is not None:
+            clip.copy('\n'.join(sel))
+
+    def paste_from_clipboard(self):
+        files = clip.paste()
+        # try add this to the list
+        try:
+            # print(files)
+            splitted_files = files.split('\n')
+            # print(splitted_files)
+            self.add_to_list(splitted_files, check_if_supported=True)
+        except:
+            # no big deal if fails
+            pass
+
+    # TODO maybe add sort by time as there is even an icon for that and can be useful for my leica files !!!
+    # TODO copy icons if they exist on natsort ok for now it's really a detail...
+    def natsort_list(self):
+        full_list = self.get_full_list()
+        if full_list is not None:
+            self.clearList()
+            self.add_to_list(natsorted(full_list), check_if_supported=False)
+
+    def clearList(self):
+        self.list.clear()
+        del self._object_dict
+        self._object_dict = {}
+
+
+if __name__ == '__main__':
+    # TODO add a main method so it can be called directly
+    # maybe just show a canvas and give it interesting props --> TODO --> really need fix that too!!!
+    import sys
+    from qtpy.QtWidgets import QApplication
+
+    # should probably have his own scroll bar embedded somewhere
+
+    app = QApplication(sys.argv)
+
+    w = ListGUI(file_to_load='/E/Sample_images/sample_images_PA/mini/list.lst')
+
+    # w.freeze(False)
+    # w.freeze(True)
+
+    w.show()
+
+    print('get_full_list', w.get_full_list())  # very good and useful
+    print('sel', w.get_selection(mode='all'))
+
+    sys.exit(app.exec_())