Update to latest Matplotlib

subplots_adjust wasn't working anymore for whatever reason, but switching to constrained layout fixed it.

Also disabled the resizing warning that was being emitted more and more often, because of autoscale being disabled automatically on things like drag and drop.

Author: rutgerkok

organoid_tracker/core/image_coloring.py

@@ -49,7 +49,7 @@ def _create_colormap(name: str) -> Colormap:
         return _create_black_to_color_colormap("magenta", (1.0, 0.0, 1.0))
     if name == "yellow":
         return _create_black_to_color_colormap("yellow", (1.0, 1.0, 0.0))
-    return matplotlib.cm.get_cmap(name)
+    return matplotlib.colormaps.get_cmap(name)
 
 
 def get_colormap(name: Optional[str]) -> Colormap:

organoid_tracker/gui/main_window.py

@@ -1,3 +1,4 @@
+import logging
 import sys
 from functools import partial
 from typing import Callable, Optional
@@ -245,10 +246,14 @@ def launch_window(experiment: Experiment) -> MainWindow:
     pyplot.rcParams["font.family"] = "Arial, sans-serif"
     pyplot.rcParams["xtick.direction"] = "in"
     pyplot.rcParams["ytick.direction"] = "in"
+    pyplot.rcParams['figure.constrained_layout.use'] = True
+
+    # Ignore "Ignoring fixed x/y limits to fulfill fixed data aspect with adjustable data limits."
+    # (Everytime any method calls .set_x/ylim, autoscale is disabled, and this warning is shown when resizing the window)
+    logging.getLogger("matplotlib.axes._base").setLevel(logging.ERROR)
 
     # Create matplotlib figure
     fig = Figure(figsize=(12, 12), dpi=95)
-    fig.subplots_adjust(left=0.04, bottom=0.04, right=0.99, top=0.98)
 
     # Create empty window
     root = QApplication.instance()

organoid_tracker/local_marginalization/tree_drawing.py

@@ -12,7 +12,7 @@
 
 
 def color_error_rates(time_point_number: int, track: LinkingTrack, experiment: Experiment) -> MPLColor:
-    _COLORMAP = matplotlib.cm.get_cmap("RdYlGn")
+    _COLORMAP = matplotlib.colormaps.get_cmap("RdYlGn")
 
     position = track.find_position_at_time_point_number(time_point_number)
 

organoid_tracker/util/mpl_helper.py

@@ -1,18 +1,18 @@
 from typing import Tuple, Optional, Union, List
 
 import numpy
-from matplotlib import colors, cm
+import matplotlib
 from matplotlib.axes import Axes
 from matplotlib.collections import LineCollection
-from matplotlib.colors import ListedColormap, Normalize
+from matplotlib.colors import ListedColormap
 
 # Colors Sander Tans likes in his figures - these are all bright colors
 # Source: flatuicolors.com - US palette
 from numpy import ndarray
 
 from organoid_tracker.core.typing import MPLColor
 
-SANDER_APPROVED_COLORS = colors.to_rgba_array(["#55efc4", "#fdcb6e", "#636e72", "#74b9ff", "#e84393",
+SANDER_APPROVED_COLORS = matplotlib.colors.to_rgba_array(["#55efc4", "#fdcb6e", "#636e72", "#74b9ff", "#e84393",
                                                "#ff7675", "#fd79a8", "#fab1a0", "#e84393"])
 
 # A bit darker colors
@@ -25,7 +25,7 @@
 HISTOGRAM_BLUE = (0, 0, 1, 0.5)
 
 def _create_qualitative_colormap() -> ListedColormap:
-    color_list = cm.get_cmap('jet', 256)(numpy.linspace(0, 1, 256))
+    color_list = matplotlib.colormaps.get_cmap('jet')(numpy.linspace(0, 1, 256))
     numpy.random.shuffle(color_list)
     color_list[0] = numpy.array([0, 0, 0, 1])  # First color is black
     return ListedColormap(color_list)

organoid_tracker/visualizer/cell_density_visualizer.py

@@ -45,7 +45,7 @@ def _calculate_densities(self):
         self._position_to_density = densities
 
     def _on_position_draw(self, position: Position, color: str, dz: int, dt: int) -> bool:
-        color_map = matplotlib.cm.get_cmap("jet")
+        color_map = matplotlib.colormaps.get_cmap("jet")
 
         density = self._position_to_density.get(position)
         density_color = "gray"

organoid_tracker/visualizer/debug_image_visualizer.py

@@ -1,4 +1,4 @@
-from matplotlib import cm
+import matplotlib
 from matplotlib.colors import Colormap
 from numpy import ndarray
 
@@ -10,7 +10,7 @@
 from organoid_tracker.visualizer.abstract_image_visualizer import AbstractImageVisualizer
 
 
-def popup_3d_image(image: ndarray, name: str, cmap: Colormap = cm.get_cmap("gray")):
+def popup_3d_image(image: ndarray, name: str, cmap: Colormap = matplotlib.colormaps.get_cmap("gray")):
     """To be used in scripts, where no GUI loop is running. After showing the image, the program exits."""
     experiment = Experiment()
     experiment.images.image_loader(SingleImageLoader(image))

organoid_tracker/visualizer/lineage_tree_visualizer.py

@@ -4,7 +4,6 @@
 
 import matplotlib.cm
 import matplotlib.colors
-import numpy
 import numpy as np
 from matplotlib.backend_bases import MouseEvent
 from mpl_toolkits.axes_grid1 import make_axes_locatable
@@ -13,7 +12,6 @@
 from organoid_tracker.core.links import LinkingTrack
 from organoid_tracker.core.position import Position
 from organoid_tracker.core.position_collection import PositionCollection
-from organoid_tracker.core.resolution import ImageTimings, ImageResolution
 from organoid_tracker.gui import dialog, option_choose_dialog
 from organoid_tracker.gui.location_map import LocationMap
 from organoid_tracker.gui.window import Window
@@ -27,7 +25,7 @@
 from organoid_tracker.position_analysis import position_markers
 from organoid_tracker.visualizer import Visualizer
 
-_SPLINE_COLORMAP = matplotlib.cm.get_cmap("YlOrBr")  # For drawing position on axis
+_SPLINE_COLORMAP = matplotlib.colormaps.get_cmap("YlOrBr")  # For drawing position on axis
 
 
 def _includes_cell_type(positions: PositionCollection, linking_track: LinkingTrack, cell_type: str):

organoid_tracker_plugins/plugin_generate_cell_tracking_configs.py

@@ -5,7 +5,7 @@
 import sys
 from typing import Dict, Optional, Any, Tuple, List
 
-import matplotlib.cm
+import matplotlib
 from matplotlib.collections import LineCollection
 
 from organoid_tracker.config import ConfigFile
@@ -480,7 +480,7 @@ def _draw_predicted_divisions(self):
         if self._predicted_divisions is None:
             return
 
-        colormap = matplotlib.cm.get_cmap("Purples")
+        colormap = matplotlib.colormaps.get_cmap("Purples")
 
         max_intensity_projection = self._display_settings.max_intensity_projection
         positions_x_list, positions_y_list, positions_face_colors, positions_edge_colors, positions_edge_widths, positions_marker_sizes = \

organoid_tracker_plugins/plugin_timings_editor.py

@@ -174,7 +174,6 @@ def draw_view(self):
             self._ax.axvline(self._max_selected_time_h, color="#00ff00", linestyle="--")
 
         self._ax.set_ylim(*self._Y_LIMITS)
-        self._fig.tight_layout()
         self._fig.canvas.draw()
 
     def _on_scroll(self, event: MouseEvent):