batoolset 0.1.0__py3-none-any.whl

batoolset/GUI/scrollablepaint.py

@@ -0,0 +1,1152 @@
+# channels seem be fixed --> cool
+# finalize whsed and corrections --> make sure they are channel dependent
+# check which channels are being restored by the new wshed within the paint arena
+from batoolset.settings.global_settings import set_UI # set the UI to qtpy
+set_UI()
+import os
+# in set image add sliders for D and Z --> see how I can do that --> or do it directly in paint ????
+import traceback
+import matplotlib.pyplot as plt
+import numpy as np
+from qtpy import QtWidgets, QtCore, QtGui
+from qtpy.QtCore import QSize, Qt
+from qtpy.QtGui import QPalette, QKeySequence, QPainter
+from qtpy.QtWidgets import QScrollArea, QVBoxLayout, QWidget, QSpinBox, QComboBox, QToolBar, QStatusBar, QLabel, \
+    QHBoxLayout, QAction, QSlider
+import qtawesome as qta
+from qtpy.QtCore import Qt, QTimer
+from batoolset.draw.shapes.freehand2d import Freehand2D
+from batoolset.draw.shapes.image2d import Image2D
+from batoolset.draw.shapes.rect2d import Rect2D
+from batoolset.img import Img, int24_to_RGB, has_metadata
+from batoolset.GUI.paint2 import Createpaintwidget
+
+# TODO --> could maybe add icons just below scroll if needed to add actions
+# j'arrive pas à creer un truc dejà self embedded
+# make it also handle other stuff
+
+# --> nb replace the Createpaintwidget in multi_image_display.py by this --> better in fact
+# shall I do full screen ???
+# TODO handle channels too if needed
+# could store mask and memory of drawing here too --> maybe on mouse release ???
+# avec des ctrl+Z et des ctrl+R
+
+
+# need zooms
+#
+
+class scrollable_paint(QWidget):
+
+    def __init__(self, custom_paint_panel=None):
+        super().__init__()
+        if custom_paint_panel is None:
+            self.paint = Createpaintwidget()
+        else:
+            self.paint = custom_paint_panel
+        layout = QVBoxLayout()
+
+        # delay dimensionality change update --> just to make sure it does not overwhelms the system upon slider change
+        # think about how to do that in a smart way -> maybe by changing the connect ???
+        # self.delayed_dimension_preview = QTimer()
+        # self.delayed_dimension_preview.setSingleShot(True)
+        # self.delayed_dimension_preview.timeout.connect(self.slider_dimension_value_changed)
+        self.dimension_sliders = []
+        self.is_width_for_alternating = True
+        # add the possibility to browse dimensions
+        self.dimensions_container = QVBoxLayout() # this will contain all the browsable dimensions of the image
+        # fake add sliders here
+        # self.dim_slider_with_label1 = self.create_dim_slider(dimension='d', max_dim=16)
+        # self.dimensions_container.addLayout(self.dim_slider_with_label1)
+        # self.dim_slider_with_label2 = self.create_dim_slider(dimension='c', max_dim=3)
+        # self.dimensions_container.addLayout(self.dim_slider_with_label2)
+        # self.dim_slider_with_label3 = self.create_dim_slider(dimension='t', max_dim=22)
+        # self.dimensions_container.addLayout(self.dim_slider_with_label3)
+        # each of the sliders will be assoc to a single dim --> TODO
+        # maybe remove the slider for channels ???
+        # same as the other with embed in scroll area
+        self.scrollArea = QScrollArea()
+        self.scrollArea.setBackgroundRole(QPalette.Dark)
+        self.scrollArea.setWidget(self.paint)
+        self.paint.scrollArea = self.scrollArea
+        layout.addLayout(self.dimensions_container)
+        layout.addWidget(self.scrollArea)
+        self.setLayout(layout)
+        status_bar = QStatusBar()
+        layout.addWidget(status_bar)
+        self.paint.statusBar = status_bar
+        self.add_shortcuts()
+        self.drawing_commands()
+
+    # this guy should handle the shortcuts it can and pass the rest to the other layer
+    def add_shortcuts(self):
+        # print('SHORTCUTS ADDED')
+
+        # if True:
+        #     return
+        zoomPlus = QtWidgets.QShortcut("Ctrl+Shift+=", self)
+        zoomPlus.activated.connect(self.zoomIn)
+        zoomPlus.setContext(QtCore.Qt.ApplicationShortcut)
+
+
+
+        # that works and disconnects all
+        # zoomPlus.disconnect()
+
+
+
+        zoomPlus2 = QtWidgets.QShortcut("Ctrl++", self)
+        zoomPlus2.activated.connect(self.zoomIn)
+        zoomPlus2.setContext(QtCore.Qt.ApplicationShortcut)
+
+        zoomMinus = QtWidgets.QShortcut("Ctrl+Shift+-", self)
+        zoomMinus.activated.connect(self.zoomOut)
+        zoomMinus.setContext(QtCore.Qt.ApplicationShortcut)
+
+        zoomMinus2 = QtWidgets.QShortcut("Ctrl+-", self)
+        zoomMinus2.activated.connect(self.zoomOut)
+        zoomMinus2.setContext(QtCore.Qt.ApplicationShortcut)
+
+        ctrl0 = QtWidgets.QShortcut("Ctrl+0", self)
+        ctrl0.activated.connect(self.zoom_reset)
+        ctrl0.setContext(QtCore.Qt.ApplicationShortcut)
+
+        self.ctrlS = QtWidgets.QShortcut("Ctrl+S", self)
+        self.ctrlS.activated.connect(self.paint.save)
+        self.ctrlS.setContext(QtCore.Qt.ApplicationShortcut)
+
+
+        self.ctrlM = QtWidgets.QShortcut("Ctrl+M", self)
+        self.ctrlM.activated.connect(self.paint.ctrl_m_apply)
+        self.ctrlM.setContext(QtCore.Qt.ApplicationShortcut)
+
+        self.shrtM = QtWidgets.QShortcut("M", self)
+        self.shrtM.activated.connect(self.paint.m_apply)
+        self.shrtM.setContext(QtCore.Qt.ApplicationShortcut)
+
+        self.increase_contrastC = QtWidgets.QShortcut('C', self)
+        self.increase_contrastC.activated.connect(self.paint.increase_contrast)
+        self.increase_contrastC.setContext(QtCore.Qt.ApplicationShortcut)
+
+        # I can connect to progeny --> makes sense and really easy --> cool
+        self.enterShortcut = QtWidgets.QShortcut(QtGui.QKeySequence(QtCore.Qt.Key_Return), self)
+        self.enterShortcut.activated.connect(self.paint.apply)
+        self.enterShortcut.setContext(QtCore.Qt.ApplicationShortcut)
+
+        self.enterShortcut2 = QtWidgets.QShortcut(QtGui.QKeySequence(QtCore.Qt.Key_Enter), self)
+        self.enterShortcut2.activated.connect(self.paint.apply)
+        self.enterShortcut2.setContext(QtCore.Qt.ApplicationShortcut)
+
+        # en fait je peux aussi connecter des trucs au descendant --> pas bete et tres facile à faire!!!
+
+        # pkoi ça ne marche pas !!!
+        self.shiftEnterShortcut = QtWidgets.QShortcut("Shift+Enter", self)
+        self.shiftEnterShortcut.activated.connect(self.paint.shift_apply)
+        self.shiftEnterShortcut.setContext(QtCore.Qt.ApplicationShortcut)
+        #
+        self.shiftEnterShortcut2 = QtWidgets.QShortcut("Shift+Return", self)
+        self.shiftEnterShortcut2.activated.connect(self.paint.shift_apply)
+        self.shiftEnterShortcut2.setContext(QtCore.Qt.ApplicationShortcut)
+
+        self.ctrl_shift_S_grab_screen_shot = QtWidgets.QShortcut('Ctrl+Shift+S', self)
+        self.ctrl_shift_S_grab_screen_shot.activated.connect(self.paint.grab_screen_shot)
+        self.ctrl_shift_S_grab_screen_shot.setContext(QtCore.Qt.ApplicationShortcut)
+
+        self.supr = QtWidgets.QShortcut(QKeySequence(Qt.Key_Delete), self)
+        self.supr.activated.connect(self.paint.suppr_pressed)
+        self.supr.setContext(QtCore.Qt.ApplicationShortcut)
+
+
+
+        # peut etre faire un fullscreen shortcut --> can be useful
+
+    def enable_shortcuts(self):
+        self.disable_shortcuts()
+        self.ctrlS.activated.connect(self.paint.save)
+        self.ctrlM.activated.connect(self.paint.ctrl_m_apply)
+        self.shrtM.activated.connect(self.paint.m_apply)
+        self.enterShortcut.activated.connect(self.paint.apply)
+        self.enterShortcut2.activated.connect(self.paint.apply)
+        self.shiftEnterShortcut.activated.connect(self.paint.shift_apply)
+        self.shiftEnterShortcut2.activated.connect(self.paint.shift_apply)
+
+    def disable_shortcuts(self):
+        # TODO
+        try:
+            self.ctrlS.disconnect()
+        except:
+            pass
+        # TODO
+        try:
+            self.ctrlM.disconnect()
+        except:
+            pass
+        try:
+            self.shrtM.disconnect()
+        except:
+            pass
+        try:
+            self.enterShortcut.disconnect()
+        except:
+            pass
+        try:
+            self.enterShortcut2.disconnect()
+        except:
+            pass
+        try:
+            self.shiftEnterShortcut.disconnect()
+        except:
+            pass
+        try:
+            self.shiftEnterShortcut2.disconnect()
+        except:
+            pass
+
+    def enableMouseTracking(self):
+        self.paint.drawing_enabled = True
+
+    def disableMouseTracking(self):
+        self.paint.drawing_enabled = False
+
+
+    # def gather_indices_for_all_dimensions(self):
+        # loop through the content of an image ????
+
+
+
+    # ça marche --> ajouter fit to width ou fit to height
+    def fit_to_width_or_height(self):
+        if self.is_width_for_alternating:
+            self.fit_to_width()
+        else:
+            self.fit_to_height()
+        self.is_width_for_alternating = not self.is_width_for_alternating
+
+    # almost there but small bugs
+    def fit_to_width(self):
+        if self.paint.image is None:
+            return
+        # self.scrollArea = self.scroll_areas[nb]
+        width = self.scrollArea.width() - 2
+        width -= self.scrollArea.verticalScrollBar().sizeHint().width()
+        # height-=self.scrollArea.horizontalScrollBar().sizeHint().height()
+        width_im = self.paint.image.width()
+        scale = width / width_im
+        self.scaleImage(scale)
+
+    def fit_to_height(self, nb=0):
+        # paint = self.paints[nb]
+        if self.paint.image is None:
+            return
+        # scrollArea = self.scroll_areas[nb]
+        height = self.scrollArea.height() - 2
+        height -= self.scrollArea.horizontalScrollBar().sizeHint().height()
+        height_im = self.paint.image.height()
+        scale = height / height_im
+        self.scaleImage(scale)
+
+    def fit_to_window(self):
+        # compute best fit
+        # just get the size of the stuff and best fit it
+        # paint = self.paints[nb]
+        if self.paint.image is None:
+            return
+
+        # QScrollArea.ensureWidgetVisible(
+        # QScrollArea.ensureVisible
+        # QScrollArea.setWidgetResizable
+        # scrollArea = self.scroll_areas[nb]
+        width = self.scrollArea.width() - 2  # required to make sure bars not visible
+        height =self. scrollArea.height() - 2
+
+        # scale image that it fits in --> change scale
+
+        # width-=self.scrollArea.verticalScrollBar().sizeHint().width()
+        # height-=self.scrollArea.horizontalScrollBar().sizeHint().height()
+
+        height_im = self.paint.image.height()
+        width_im = self.paint.image.width()
+        scale = height / height_im
+        if width / width_im < scale:
+            scale = width / width_im
+        self.scaleImage(scale)
+
+
+
+
+    def zoomIn(self):
+        # 10% more each time
+        self.scaleImage(self.paint.scale + (self.paint.scale*10.0/100.0))# une hausse de 10% à chaque fois
+
+    def zoomOut(self):
+        # 10% less each time
+        self.scaleImage(self.paint.scale - (self.paint.scale*10.0/100.0))
+
+    def zoom_reset(self):
+        # resets zoom
+        self.scaleImage(1.0)
+
+    # pb this is redundant with the main GUI and not in sync --> can cause a lot of trouble --> dactivate for now
+    def full_screen(self):
+            if not self.isFullScreen():
+                self.fullscreen.setIcon(qta.icon('mdi.fullscreen-exit'))
+                self.fullscreen.setToolTip('Exit full screen')
+                self.showFullScreen()
+                # self.setWindowFlags(
+                #     QtCore.Qt.Window |
+                #     QtCore.Qt.CustomizeWindowHint |
+                #     # QtCore.Qt.WindowTitleHint |
+                #     # QtCore.Qt.WindowCloseButtonHint |
+                #     QtCore.Qt.WindowStaysOnTopHint
+                # )
+            else:
+                # settings = QSettings()
+                # self.Stack.restoreGeometry(settings.value("geometry")) #.toByteArray()
+                self.fullscreen.setIcon(qta.icon('mdi.fullscreen'))
+                self.fullscreen.setToolTip('Enter full screen')
+                self.setWindowFlags(QtCore.Qt.Widget)
+                # # self.Stack.setWindowFlags(self.flags)
+                # self.grid.addWidget(self.Stack, 0,
+                #                     0)  # pas trop mal mais j'arrive pas à le remettre dans le truc principal
+                # # dirty hack to make it repaint properly --> obviously not all lines below are required but some are --> need test, the last line is key though
+                # self.grid.update()
+                # self.Stack.update()
+                # self.Stack.show()
+                # self.centralWidget().setLayout(self.grid)
+                # self.centralWidget().update()
+                # self.update()
+                self.show()
+                self.repaint()
+                # self.Stack.update()
+                # self.Stack.repaint()
+                # self.centralWidget().repaint()
+
+    def scaleImage(self, scale):
+        self.paint.set_scale(scale)
+        if self.paint.image is not None:
+            self.paint.resize(self.paint.scale * self.paint.image.size())
+        else:
+            self.paint.resize(QSize(0, 0))
+        self.paint.update()
+
+    # can maybe add pen stuff here --> simpler and easier
+    # need zoom buttons here too
+    '''
+    buttons/icons to add at some point
+    
+        
+        "Cell smaller than this value will be destroyed"
+        "small_cell_remover"
+        
+        
+        "/Icons/refresh.png"
+        "run 2 seeds watershed (click twice in a poorly segmented cell to have a the bond be created using the watershed algorithm)"
+        
+        "/Icons/Knob Snapback.png"
+        "Undo"
+        
+        "/Icons/Knob Valid Blue.png"
+        "remove small cells and apply correction"
+        
+        "/Icons/Knob Valid Green.png"
+        "apply correction"
+        
+        "/Icons/channels.png"
+        "Channel Selection"
+        "Channel to use for Watershed, polarity, recentering,...")
+        
+        "/Icons/onebit_11.png"
+        "Save"
+        
+        
+        "/Icons/eye.png"
+        "View below the mask (lasts 2s)"
+        
+        
+        "/Icons/zoom in.png"
+        "Zoom +"
+        
+        "/Icons/zoom out.png"
+        "Zoom -"
+        
+        "/Icons/1in1.png"
+        "1:1 aspect ratio"
+        
+        "/Icons/fit_2_screen.gif"
+        "Fit to panel"
+        
+        
+        "/Icons/double_diagonal_arrow.gif"
+        "Alternate between best fit in height or in width"
+        
+        
+        "/Icons/Import Picture Document.png"
+        "Send Current View To The System Clipboard"
+        
+        "/Icons/pipet_small.png"
+        "Color pipet"
+        
+        "Mask col"
+        "mask color"
+        
+        "Correct Drift" 
+    
+    '''
+
+    # add shortcut for show hide mask and maybe also full screen --> not a good idea
+
+    def drawing_commands(self):
+        self.penSize = QSpinBox(objectName='penSize')
+        self.penSize.setToolTip('Change this value to change pen size')
+        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.setToolTip('Select the channel of interest')
+        self.channels.addItem("merge")
+        # self.channels.addItem("0")
+        # self.channels.addItems(["1", "2", "3"])
+        self.channels.currentIndexChanged.connect(self.channelChange)
+
+
+        hlayout_of_toolbars = QHBoxLayout()
+        hlayout_of_toolbars.setAlignment(Qt.AlignLeft)
+        self.tb1 = QToolBar()
+        self.tb2 = QToolBar()
+        self.tb3 = QToolBar()
+
+
+        pencil_action = QAction(qta.icon('ei.pencil'), 'Pen Size', self)
+        pencil_action.setEnabled(False)
+        self.tb2.addAction(pencil_action)
+        # tb.addAction("sq...")
+        self.tb2.addWidget(self.penSize)
+
+        # toolButton = QToolButton()
+        # toolButton.setText("Draw")
+        # toolButton.setIcon(self.style().standardIcon(QStyle.SP_DriveFDIcon))
+        # tb.addWidget(toolButton)
+
+        # fa5.save
+        save_action = QAction(qta.icon('fa5.save'), 'Save mask', self)
+        save_action.triggered.connect(self.paint.save)
+        self.tb2.addAction(save_action)
+
+
+        # toolButton2 = QToolButton()
+        # toolButton2.setText("Draw")
+        # toolButton2.setIcon(self.style().standardIcon(QStyle.SP_DialogApplyButton))
+        # tb.addWidget(toolButton2)
+
+
+        show_hide_mask =QAction(qta.icon('fa.bullseye'), 'Show/hide mask (same as pressing "M")', self)
+        show_hide_mask.triggered.connect(self.paint.m_apply)
+        self.tb2.addAction(show_hide_mask)
+
+        apply_drawing = QAction(qta.icon('fa.check'), 'Apply drawing (same as pressing the "Enter" key)', self)
+        apply_drawing.triggered.connect(self.paint.apply)
+        self.tb2.addAction(apply_drawing)
+
+        # 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("Draw")
+        # toolButton5.setIcon(self.style().standardIcon(QStyle.SP_TrashIcon))
+        # tb.addWidget(toolButton5)
+
+        # toolButton6 = QToolButton()
+        # toolButton6.setText("Draw")
+        # toolButton6.setIcon(self.style().standardIcon(QStyle.SP_ArrowBack))
+        # tb.addWidget(toolButton6)
+
+        # toolButton7 = QToolButton()
+        # toolButton7.setText("Draw")
+        # toolButton7.setIcon(self.style().standardIcon(QStyle.SP_BrowserReload))
+        # tb.addWidget(toolButton7)
+
+        self.small_cell_size = QSpinBox()
+        self.small_cell_size.setToolTip('Select the minimal pixel area for a cell to be considered as a cell.\nAny cell having an area less than this value will be removed.')
+        self.small_cell_size.setSingleStep(1)
+        self.small_cell_size.setRange(1, 1000000)
+        self.small_cell_size.setValue(10)
+        self.small_cell_size.valueChanged.connect(self.small_cell_size_changed)
+
+        self.tb2.addWidget(self.small_cell_size)
+        apply_rm_small_cells = QAction(qta.icon('mdi.check-underline'), 'Apply drawing and remove small cells (same as pressing "Shift+Enter")', self)
+        apply_rm_small_cells.triggered.connect(self.paint.shift_apply)# self.paint.shift_apply
+        self.tb2.addAction(apply_rm_small_cells)
+
+
+
+
+
+        # marche pas --> comment faire pr que ça marche...
+        local_reshed = QAction(qta.icon('mdi.reload'), 'Locally seeded watershed (same as pressing "Ctrl/Cmd + M")', self)
+        local_reshed.triggered.connect(self.paint.ctrl_m_apply)# self.paint.shift_apply
+        self.tb2.addAction(local_reshed)
+        # hgjhghj
+
+        # toolButton8 = QToolButton()
+        # toolButton8.setText("Zoom+")
+        # toolButton8.setIcon(qta.icon('ei.zoom-in')) # mdi.magnify-plus-outline --> marche aussi
+        # tb.addWidget(toolButton8)
+
+        # toolButton9 = QToolButton()
+        # toolButton9.setText("Zoom-")
+        # toolButton9.setIcon(qta.icon('ei.zoom-out'))
+        # tb.addWidget(toolButton9)
+
+        zoom_plus = QAction(qta.icon('ei.zoom-in'), 'Zoom+', self)
+        zoom_plus.triggered.connect(self.zoomIn)
+        self.tb1.addAction(zoom_plus)
+
+        zoom_minus = QAction(qta.icon('ei.zoom-out'), 'Zoom-', self)
+        zoom_minus.triggered.connect(self.zoomOut)
+        self.tb1.addAction(zoom_minus)
+
+
+        zoom_width_or_height = QAction(qta.icon('mdi.fit-to-page-outline'), 'Alternates between best fit in width and height', self)
+        zoom_width_or_height.triggered.connect(self.fit_to_width_or_height)
+        self.tb1.addAction(zoom_width_or_height)
+
+        zoom_0 = QAction(qta.icon('ei.resize-full'), 'Reset zoom', self)
+        zoom_0.triggered.connect(self.zoom_reset)
+        self.tb1.addAction(zoom_0)
+
+        # redundant with TA full screen and not in sync --> disable for now
+        # self.fullscreen = QtWidgets.QAction(qta.icon('mdi.fullscreen'), 'Full screen', self)
+        # self.fullscreen.setToolTip('Enter full screen')
+        # self.fullscreen.triggered.connect(self.full_screen)
+        # self.tb1.addAction(self.fullscreen)
+
+
+
+
+        # exit_fullscreen = QtWidgets.QAction(qta.icon('mdi.fullscreen'), 'Full screen', self)
+        # exit_fullscreen.triggered.connect(self.showFullScreen)
+        # self.tb1.addAction(fullscreen)
+
+
+
+        self.channel_label = QLabel('Channels:')
+        self.channel_label.setToolTip('Select the channel of interest')
+        self.tb3.addWidget(self.channel_label)
+        self.tb3.addWidget(self.channels)
+
+        # mdi.fullscreen
+        # mdi.fullscreen-exit
+        # ei.fullscreen --> a bit less good I find
+        # fa.bullseye
+
+        # could have show and hide mask here --> see how I can do that --> but do not delete it in fact
+
+        # self.layout().addWidget(self.tb1)
+        hlayout_of_toolbars.addWidget(self.tb2)
+
+
+        # self.tb2.addAction('toto')
+        # self.tb2.addAction('ttutu')
+        # self.tb2.addAction('tata')
+        hlayout_of_toolbars.addWidget(self.tb3)
+
+
+        # one for the zooms
+        # one for drawing and apply different things
+        # TODO do several toolbars to deactivate different levels of stuff
+        # and only allow save in the appropriate stuff
+
+        # self.tb3.addAction('toto')
+        # self.tb3.addAction('ttutu')
+        # self.tb3.addAction('tata')
+        hlayout_of_toolbars.addWidget(self.tb1)
+
+        self.layout().addLayout(hlayout_of_toolbars)
+
+    def get_selected_channel(self):
+        idx = self.channels.currentIndex()
+        if idx == 0:
+            return None
+        else:
+            return idx-1
+
+    # TODO also implement channel change directly within the display tool
+    # if merge is applied --> apply on average of all channels --> maybe not so smart an idea but ok to start with and better than what I do in TA
+    def channelChange(self, i):
+        # update displayed image depending on channel
+        # dqqsdqsdqsd
+        # pass
+        # try change channel if
+
+
+        # tODO --> need at least to reactivate a bit that
+        # pass
+        # print('in channel change') # needs a fix
+        meta = None
+        try:
+            meta = self.paint.raw_image.metadata
+        except:
+            pass
+        self.paint.set_display(self.get_image_to_display_including_all_dims(), metadata=meta)
+        self.paint.channelChange(i, skip_update_display=True)
+
+        # print('in channel change !!!')
+        # if self.img is not None:
+        #     # print('in', self.img.metadata)
+        #     if self.Stack.currentIndex() == 0:
+        #         # need copy the image --> implement that
+        #         # print(self.img[..., i].copy())
+        #         # print(self.img[..., i])
+        #         if i == 0:
+        #             self.paint.setImage(self.img)
+        #             # print('original', self.img.metadata)
+        #         else:
+        #             # print('modified0', self.img.metadata)
+        #             channel_img = self.img.imCopy(c=i - 1)  # it's here that it is affected
+        #             # print('modified1', self.img.metadata)
+        #             # print('modified2', channel_img.metadata)
+        #             self.paint.setImage(channel_img)
+        #         self.paint.update()
+        # else:
+        #     # logger.error("Not implemented yet TODO add support for channels in 3D viewer")
+        #     # sdqdqsdsqdqsd
+        #     self.loadVolume()
+        # or reimplement that for multi channels !!!
+
+
+
+    # TODO maybe handle pen size change directly within the display --> can be useful by the way
+    def small_cell_size_changed(self):
+        self.paint.minimal_cell_size = self.small_cell_size.value()
+
+    # TODO maybe handle pen size change directly within the display --> can be useful by the way
+    def penSizechange(self):
+        self.paint.brushSize = self.penSize.value()
+        # self.update() # too slow if I update --> avoid
+        # self.l1.setFont(QFont("Arial", size))
+
+    def set_image(self, img):
+        # probably I need store raw image to avoid issues --> TODO ???
+        self.paint.set_image(img)# bug seems to be here
+
+        img = self.paint.raw_image
+
+        self.update_image_dimensions()
+
+        # need also update the dimensions if any
+
+        # print(type(img))
+
+        # else I need also reset channels
+
+        # if img is not None:
+        #     if img.has_c():
+        self._update_channels(img=img)
+        # print('out')
+        # channels = self.paint.get_nb_channels()
+        # self._update_channels(channels)
+        # make it update also the channels
+    def _delete_layout_content(self, layout):
+        for i in reversed(range(layout.count())):
+            layout.itemAt(i).widget().setParent(None)
+
+
+
+    # centralized version of the thing
+    def get_image_to_display_including_all_dims(self):
+        # print('in get_image_to_display_including_all_dims')
+        # returns the image to be displayed --> takes into account all the dimensions at once
+
+        #
+        # if self.raw_image is not None:
+        #     if i == 0:
+        #         self.set_display(self.raw_image)
+        #         self.channel = None
+        #         # print('original', self.img.metadata)
+        #     else:
+        #         # print('modified0', self.img.metadata)
+        #         # I need a hack when the image is single channel yet I need several masks for it !!!
+        #         if self.multichannel_mode and i - 1 >= self.raw_image.shape[-1]:
+        #             channel_img = self.raw_image.imCopy(c=0)  # if out of bonds load the first channel
+        #         else:
+        #             channel_img = self.raw_image.imCopy(c=i - 1)  # it's here that it is affected
+        #         self.channel = i - 1
+        #         # print('modified1', self.img.metadata)
+        #         # print('modified2', channel_img.metadata)
+        #         self.set_display(
+        #             channel_img)  # maybe do a set display instead rather --> easier to handle --> does a subest of the other
+        image_to_display = None
+        try:
+            # need change just the displayed image
+            if has_metadata(self.paint.raw_image) and self.paint.raw_image.metadata['dimensions']:
+                # change the respective dim
+                # need all the spinner values to be recovered in fact
+                # and send the stuff
+                # print('dimension exists', self.objectName(),'--> changing it')
+
+                # need gather all the dimensions --> TODO
+                dimensions = self.paint.raw_image.metadata['dimensions']
+                position_h = dimensions.index('h')
+                image_to_display = self.paint.raw_image
+                if position_h != 0:
+                    # loop for all the dimensions before
+                    # print('changing stuff')
+                    for pos_dim in range(0, position_h):
+                        dim = dimensions[pos_dim]
+                        value_to_set = self.get_dim_value_by_name(dim)
+                        if value_to_set == None:
+                            continue
+                        else:
+                            image_to_display = image_to_display[value_to_set]
+                        # if not dimensions[pos_dim]==self.sender().objectName():
+                        #     image_to_display = image_to_display[0]
+                        # else:
+                        #     image_to_display = image_to_display[self.sender().value()]
+                # self.paint.set_display(image_to_display)
+                channel_to_display = self.get_selected_channel()
+
+                # if force dimensions --> I need a hack even if
+                # hack for GT image editor --> where nb of channels are forced and do not necessarily match the channels of the image --> is that smart to put that here ???
+                if channel_to_display is not None and 'c' in dimensions:
+                    if self.paint.multichannel_mode and channel_to_display >= self.paint.raw_image.shape[-1]:
+                        image_to_display = image_to_display[..., 0]
+                    else:
+                        image_to_display=image_to_display[...,channel_to_display]
+                    # print(image_to_display.shape)
+        except:
+            traceback.print_exc()
+        return image_to_display
+
+    def update_image_dimensions(self):
+        self.dimension_sliders = []
+
+        for i in reversed(range(self.dimensions_container.count())):
+            # print(i)
+            # print(self.dimensions_container.itemAt(i))
+            # self.dimensions_container.itemAt(i).widget().setParent(None)
+            self._delete_layout_content(self.dimensions_container.itemAt(i))
+
+        if self.paint.raw_image is None:
+            return
+
+        # empty the content of the slider and refill it
+        try:
+            treat_channels_as_a_browsable_dimension = False
+            if has_metadata(self.paint.raw_image):
+                dimensions = self.paint.raw_image.get_dimensions_as_string()
+
+                # if not self.paint.raw_image.has_c():
+                #     nb_of_sliders = len(
+                #         self.paint.raw_image.shape) - 2  # or -3 it depends whether I wanna show all the channels at once or not ???
+                # else:
+                #     nb_of_sliders = len(
+                #         self.paint.raw_image.shape) - 2  # or -3 it depends whether I wanna show all the channels at once or not ???
+
+                # print(nb_of_sliders)
+
+                # create an image with plenty of sliders --> TODO
+                # make the handling of the image to be displayed directly by the code !!!
+
+                # then I need couple each slider to a dimension
+
+                # dimensions that must have a slider
+                # --> all dimensions but hw and maybe c must have a slider --> TODO
+                for dim in dimensions:
+                    if dim == 'h' or dim == 'y' or dim == 'w' or dim == 'x' or (
+                            not treat_channels_as_a_browsable_dimension and dim == 'c'):
+                        # we skip dimensions
+                        continue
+                    # print(dim, 'must have an assoicated slider')
+
+                    # print(self.paint.raw_image.shape, ' toto ', )
+                    self.dimensions_container.addLayout(self.create_dim_slider(dimension=dim, max_dim=self.paint.raw_image.shape[dimensions.index(dim)]))
+        except:
+            traceback.print_exc()
+
+    def set_mask(self, mask):
+        self.paint.set_mask(mask)
+
+    def _update_channels(self, img):
+        selection = self.channels.currentIndex()
+        self.channels.disconnect()
+        self.channels.clear()
+        comboData = ['merge']
+        if img is not None:
+            try:
+                if img.has_c():
+                    for i in range(img.get_dimension('c')):
+                        comboData.append(str(i))
+            except:
+                # assume image has no channel and return None
+                # or assume last stuff is channel if image has more than 2
+                pass
+        # logger.debug('channels found ' + str(comboData))
+        self.channels.addItems(comboData)
+        # index = self.channels.findData(selection)
+
+        self.channels.currentIndexChanged.connect(self.channelChange)
+        # print("data", index)
+        if selection != -1 and selection < self.channels.count():
+            self.channels.setCurrentIndex(selection)
+            # self.channelChange(selection)
+        else:
+            self.channels.setCurrentIndex(0)
+            # self.channelChange(0)
+
+
+    def freeze(self, bool, level=1):
+
+        self.tb1.setEnabled(True)
+        self.tb2.setEnabled(True)
+        self.tb3.setEnabled(True)
+
+        if level == 1:
+            self.tb2.setEnabled(not bool)
+        elif level == 2:
+            self.tb2.setEnabled(not bool)
+            self.tb3.setEnabled(not bool)
+
+        if bool:
+            self.disable_shortcuts()
+        else:
+            self.enable_shortcuts()
+        # remove draw mode maybe and freeze shortcuts
+
+    def create_dim_slider(self, dimension=None, max_dim=1):
+        dim_slider_with_label1 = QHBoxLayout()
+        label_slider1 = QLabel()
+        if dimension is not None:
+            label_slider1.setText(dimension)
+        fake_dim_slider = QSlider(Qt.Horizontal)
+        fake_dim_slider.setMinimum(0)
+        fake_dim_slider.setMaximum(max_dim-1)
+        dim_slider_with_label1.addWidget(label_slider1)
+        dim_slider_with_label1.addWidget(fake_dim_slider)
+        # dim_slider_with_label1
+        # add a partial?
+        fake_dim_slider.valueChanged.connect(self.slider_dimension_value_changed)
+        # fake_dim_slider.valueChanged.connect(lambda x: self.delayed_dimension_preview.start(600))
+        fake_dim_slider.setObjectName(dimension)
+        self.dimension_sliders.append(fake_dim_slider)
+        return dim_slider_with_label1
+
+    def get_dim_value_by_name(self, label):
+        for slider in self.dimension_sliders:
+            if slider.objectName() == label:
+                return slider.value()
+        return None
+
+    # def get_dims_value_by_name(self, label):
+    #     for slider in self.dimension_sliders:
+    #         if slider.objectName() == label:
+    #             return slider.value()
+    #     return None
+
+    # p
+    def slider_dimension_value_changed(self):
+        # TODO --> do delay only if necessary
+        # self.delayed_dimension_preview.stop()
+        # self.delayed_dimension_preview.start(600)
+
+        # self.delayed_dimension_preview.timeout.connect
+
+        # if self.delayed_dimension_preview.dis
+
+        # TODO only allow this when the dimension changing is over
+        # if the dimension exists --> print it
+        # print(self.sender(), self.sender().objectName(), self.sender().value())
+        # print(self.sender(), self.sender().objectName())
+        # print(sender)
+        #
+        # try:
+        #     # need change just the displayed image
+        #     if self.paint.raw_image.metadata['dimensions']:
+        #         # change the respective dim
+        #         # need all the spinner values to be recovered in fact
+        #         # and send the stuff
+        #         # print('dimension exists', self.objectName(),'--> changing it')
+        #
+        #         # need gather all the dimensions --> TODO
+        #         dimensions = self.paint.raw_image.metadata['dimensions']
+        #         position_h =  dimensions.index('h')
+        #         image_to_display = self.paint.raw_image
+        #         if position_h!=0:
+        #             # loop for all the dimensions before
+        #             # print('changing stuff')
+        #             for pos_dim in range(0,position_h):
+        #                 dim = dimensions[pos_dim]
+        #                 value_to_set = self.get_dim_value_by_name(dim)
+        #                 if value_to_set == None:
+        #                     continue
+        #                 else:
+        #                     image_to_display = image_to_display[value_to_set]
+        #                 # if not dimensions[pos_dim]==self.sender().objectName():
+        #                 #     image_to_display = image_to_display[0]
+        #                 # else:
+        #                 #     image_to_display = image_to_display[self.sender().value()]
+        #         self.paint.set_display(image_to_display)
+        # except:
+        #     traceback.print_exc()
+
+        try:
+            meta = None
+            try:
+                meta = self.paint.raw_image.metadata
+            except:
+                pass
+            # metadata is required to get the luts properly
+            self.paint.set_display(self.get_image_to_display_including_all_dims(), metadata=meta)
+        except:
+            traceback.print_exc()
+
+        # pass
+
+    # then have a single code to handle dynamically all the dimension changes !!! --> TODO
+
+
+# pas mal faut juste voir ce que je peux faire
+# peut etre permetre de mettre des custom panels
+
+if __name__ == '__main__':
+    import sys
+    from qtpy.QtWidgets import QApplication
+
+
+    # hand drawing panel
+    if False:
+
+        # 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!!!
+
+
+        # should probably have his own scroll bar embedded somewhere
+
+        app = QApplication(sys.argv)
+
+
+        # quite easy todo in fact
+
+        # no clue why it always works just once
+
+
+        # maybe make a scrollable TA paint that will handle and behave like that
+        # maybe handle also stacks at some point ---> see how
+        # --> almost all is ok now
+        class overriding_apply(Createpaintwidget):
+            # all seems ok now and functions as in TA
+            # just do the shift enter to get rid of small cells
+
+            # avec ça ça marche 100% à la TA ... --> cool --> maybe make it a TA drawing pad
+            def apply(self):
+               self.apply_drawing(minimal_cell_size=0)
+
+            def shift_apply(self):
+                # MEGA TODO IMPLEMENT SIZE within this stuff!!!
+                self.apply_drawing(minimal_cell_size=10)
+
+            def ctrl_m_apply(self):
+                self.manually_reseeded_wshed()
+
+            def save(self):
+                self.save_mask()
+
+        w = scrollable_paint(
+            custom_paint_panel=overriding_apply())  # ça marche --> permet de mettre des paint panels avec des proprietes particulieres --> assez facile en fait
+        # w.set_image('/E/Sample_images/sample_images_PA/mini (copie)/focused_Series012.png')
+        # w.set_mask('/E/Sample_images/sample_images_PA/mini (copie)/focused_Series012/handCorrection.png')
+        # w.set_image('/E/Sample_images/sample_images_PA/test_complete_wing_raphael/Optimized_projection_018.png')
+        # w.set_mask('/E/Sample_images/sample_images_PA/test_complete_wing_raphael/neo_mask.tif')
+
+        w.set_image('/D/VirtualBox/book_chapter_image_segmentation_final_2021/new_figs/dataset_1/minimal_demo_sample_simplified_bckup_before_messing_with_two_seg_errors/1.tif')
+        w.set_mask('/D/VirtualBox/book_chapter_image_segmentation_final_2021/new_figs/dataset_1/minimal_demo_sample_simplified_bckup_before_messing_with_two_seg_errors/1/handCorrection.tif')
+
+
+        # ça marche mais tt finalizer
+        # that seems to work
+
+        # w.freeze(True)
+        # w.freeze(False)
+        # w.freeze(True)
+
+        # all is so easy to do this way
+
+        # ça marche --> tres facile a tester
+        # --> how can I do a zoom
+        # ask whether self scroll or not --> if scrollable
+
+        # mask = w.get_mask()
+        #
+        # plt.imshow(mask)
+        # plt.show()
+
+        w.show()
+        sys.exit(app.exec_())
+
+    # vectorial panel for drawing ROIs --> that works --> keep this code cause very useful and many bug fix
+    # TODO try convert any ROIs to something like a contour using the pavlidis algo --> put this in rps tools
+
+    if True:
+        # 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!!!
+
+        # should probably have his own scroll bar embedded somewhere
+
+        app = QApplication(sys.argv)
+
+
+        # quite easy todo in fact
+
+        # no clue why it always works just once
+
+        # maybe make a scrollable TA paint that will handle and behave like that
+        # maybe handle also stacks at some point ---> see how
+        # --> almost all is ok now
+        class overriding_apply(Createpaintwidget):
+            # all seems ok now and functions as in TA
+            # just do the shift enter to get rid of small cells
+            def m_apply(self):
+                self.vdp.active = not self.vdp.active
+                self.update()
+
+            # avec ça ça marche 100% à la TA ... --> cool --> maybe make it a TA drawing pad
+            def apply(self):
+                # self.apply_drawing(minimal_cell_size=0)
+                pass
+
+            def shift_apply(self):
+                # MEGA TODO IMPLEMENT SIZE within this stuff!!!
+                # self.apply_drawing(minimal_cell_size=10)
+                pass
+
+            def ctrl_m_apply(self):
+                # print('seed')
+                # self.manually_reseeded_wshed()
+                pass
+
+            def save(self):
+                # self.save_mask()
+                print('saving ROIs')
+                print(self.vdp.shapes)
+                # create an image the save size as the displayed one and open it
+                if self.raw_image is None:
+                    return
+                if len(self.raw_image.shape)==2:
+                    black_image = np.zeros_like(self.raw_image, dtype=np.uint64)
+                else:
+                    black_image = np.zeros(shape=(*self.raw_image[:-1],), dtype=np.uint64)
+                # plt.imshow(black_image)
+                # plt.show()
+                # make it fill all the ROIs inside that
+                im2d = Image2D(black_image)
+
+                for iii,shape in enumerate(self.vdp.shapes):
+                    # ideally need clone it and make it the enumerate color +1
+
+                    shape.fill_color = iii+1
+                    shape.color = None
+                    # print(shape.fill_color)
+                    # print(type(shape), shape.fill_color)
+                    im2d.annotation.append(shape)
+
+
+
+                # im2d.annotation.extend(self.vdp.shapes)
+
+                # need clone the shape
+
+                # I need remove antialiasing
+                im = im2d.save(None,quality=QPainter.NonCosmeticDefaultPen)
+                im = im2d.convert_qimage_to_numpy(im)
+
+                # restore colors
+                for shape in self.vdp.shapes:
+                    shape.fill_color = None
+                    shape.color = 0xFFFFFF
+
+                # faudrait tester en grandeur reelle pr voir si ça marche --> à faire !!!
+                if True:
+                    # TODO just save the raw file in one channel not in many --> check the  output by the way
+
+                    # from skimage.measure import label
+                    # lab = label(im, connectivity=2, background=0)
+                    # im=lab
+
+                    # I need remove antialiasing
+                    Img(im.astype(np.float64), dimensions='hwc').save('/E/Sample_images/sample_image_neurons_laurence_had/data_test/test_raw.tif')
+
+                    plt.imshow(im)
+                    plt.show()
+
+                # what I need to do here now is to save in the folder of the parent à la TA --> can save it as neurons.tif maybe
+
+
+
+
+            # def suppr_pressed(self):
+            #     # self.save_mask()
+            #     # print('suppr')
+            #     self.pa
+
+
+        test = overriding_apply()
+        test.vdp.shape_to_draw = Freehand2D
+
+        # test.vdp.shape_to_draw = Rect2D # ça ça marche --> bug is in the other then...
+
+        # there is a bug in the vectorial but no big deal probably
+
+        w = scrollable_paint(
+            custom_paint_panel=test)  # ça marche --> permet de mettre des paint panels avec des proprietes particulieres --> assez facile en fait
+        # w.set_image('/E/Sample_images/sample_images_PA/mini (copie)/focused_Series012.png')
+        # w.set_mask('/E/Sample_images/sample_images_PA/mini (copie)/focused_Series012/handCorrection.png')
+        # w.set_image('/E/Sample_images/sample_images_PA/test_complete_wing_raphael/Optimized_projection_018.png')
+        # w.set_mask('/E/Sample_images/sample_images_PA/test_complete_wing_raphael/neo_mask.tif')
+
+        test.vdp.active = True
+        test.vdp.drawing_mode = True
+
+        # QApplication.setOverrideCursor(Qt.WaitCursor)
+        # do lengthy process
+        # QApplication.restoreOverrideCursor()
+
+        # w.set_image('/E/Sample_images/sample_images_FIJI/sample2.lsm')
+        w.set_image('/E/Sample_images/sample_images_denoise_manue/29-1_lif/ON 290119.lif - Series001.tif')
+
+        # w.set_image('/E/Sample_images/sample_image_neurons_laurence_had/data_test/image.png')
+        # w.set_mask('/D/VirtualBox/book_chapter_image_segmentation_final_2021/new_figs/dataset_1/minimal_demo_sample_simplified_bckup_before_messing_with_two_seg_errors/1/handCorrection.tif')
+
+        # w.setCursor(Qt.BlankCursor)
+
+        # ça marche mais tt finalizer
+        # that seems to work
+
+        # w.freeze(True)
+        # w.freeze(False)
+        # w.freeze(True)
+
+        # we force the cursor to be visible --> set it by default
+        # cursor = Qt.ArrowCursor
+        # w.paint.setCursor(cursor)
+
+        # all is so easy to do this way
+
+        # ça marche --> tres facile a tester
+        # --> how can I do a zoom
+        # ask whether self scroll or not --> if scrollable
+
+        # mask = w.get_mask()
+        #
+        # plt.imshow(mask)
+        # plt.show()
+
+        w.show()
+        # w.setCursor(Qt.BlankCursor)
+        sys.exit(app.exec_())