Windowing histogram (#298)

* Add files via upload

* Revert "Add files via upload"

This reverts commit 6b39071.

* Added histogram.
Histogram updates to selected slice.
In 3D view, it syncs to the Axial view.
The seperate views cannot support their own windowing sliders until the way windowing is handled is changed to accomodate individual slice windowing.

---------

Co-authored-by: Daniel Horton <danielhorton4001>

src/Controller/ActionHandler.py

@@ -380,6 +380,8 @@ def one_view_handler(self):
         self.__main_page.dicom_single_view.update_view()
         self.__main_page.dicom_single_view_layout.addWidget(
             self.__main_page.windowing_slider, 0, 0)
+        self.__main_page.windowing_slider.set_dicom_view(
+            self.__main_page.dicom_single_view)
 
         if hasattr(self.__main_page, 'image_fusion_view'):
             self.has_image_registration_four = False
@@ -398,6 +400,8 @@ def four_views_handler(self):
         self.__main_page.dicom_axial_view.update_view()
         self.__main_page.dicom_four_views_slider_layout.addWidget(
             self.__main_page.windowing_slider, 0, 0)
+        self.__main_page.windowing_slider.set_dicom_view(
+            self.__main_page.dicom_axial_view)
 
         if hasattr(self.__main_page, 'image_fusion_view'):
             self.has_image_registration_four = True

src/View/mainpage/DicomView.py

@@ -34,6 +34,7 @@ def __init__(self, roi_color=None, iso_color=None, cut_line_color=None):
         self.vertical_view = None
         self.cut_lines_color = cut_line_color
         self.dicom_view_layout = QtWidgets.QHBoxLayout()
+        self.windowing_slider = None
 
         # Create components
         self.slider = QtWidgets.QSlider(QtCore.Qt.Vertical)
@@ -108,6 +109,8 @@ def value_changed(self):
         if self.horizontal_view is not None and self.vertical_view is not None:
             self.horizontal_view.update_view()
             self.vertical_view.update_view()
+        if self.windowing_slider is not None:
+            self.windowing_slider.update_density_histogram()
 
     def update_view(self, zoom_change=False):
         """

src/View/mainpage/MainPage.py

@@ -165,7 +165,7 @@ def setup_central_widget(self):
             roi_color=roi_color_dict, iso_color=iso_color_dict,
             cut_line_color=QtGui.QColor(0, 0, 255))
         self.three_dimension_view = DicomView3D()
-        self.windowing_slider = WindowingSlider()
+        self.windowing_slider = WindowingSlider(self.dicom_single_view)
 
         # Rescale the size of the scenes inside the 3-slice views
         self.dicom_axial_view.zoom = INITIAL_FOUR_VIEW_ZOOM

src/View/mainpage/WindowingSlider.py

@@ -1,23 +1,11 @@
 from src.Model.PatientDictContainer import PatientDictContainer
+from src.Model.Windowing import windowing_model_direct, set_windowing_slider
 from PySide6.QtWidgets import QWidget, QLabel, QApplication, QGridLayout, QSizePolicy
 from PySide6.QtCharts import QChart, QChartView, QLineSeries, QHorizontalBarSeries, QBarSet
 from PySide6.QtGui import QPixmap, QPainter
 from PySide6 import QtCore
 from math import ceil
-
-from src.Model.Windowing import windowing_model_direct, set_windowing_slider
-
-import random
-
-
-def gen_random_histogram():
-    """
-    Temporary function to populate histogram
-    """
-    d = [0.5]
-    for n in range(0, 599):
-        d.append((d[-1] + random.random()) * random.random())
-    return d
+import numpy as np
 
 
 class WindowingSlider(QWidget):
@@ -38,9 +26,10 @@ class WindowingSlider(QWidget):
 
     SINGLETON = None
 
-    def __init__(self, width=50):
+    def __init__(self, dicom_view, width=50):
         """
         Initialise the slider
+        :param dicom_view: A DICOM View
         :param width: the fixed width of the widget
         """
 
@@ -50,6 +39,10 @@ def __init__(self, width=50):
             WindowingSlider.SINGLETON = self
             set_windowing_slider(self)
 
+        self.set_dicom_view(dicom_view)
+        patient_dict_container = PatientDictContainer()
+        self.pixel_values = patient_dict_container.get("pixel_values")
+
         # Manage size of whole widget
         self.fixed_width = width
         self.size_policy = QSizePolicy()
@@ -59,18 +52,18 @@ def __init__(self, width=50):
         self.setFixedWidth(self.fixed_width)
 
         # Histogram
+        self.densities = None
         self.histogram_view = HistogramChart(self)
         self.histogram_view.windowing_slider = self
         self.histogram = QChart()
         self.histogram_view.setChart(self.histogram)
         self.histogram.setPlotArea(
-            QtCore.QRectF(0, 0, self.fixed_width, self.height()))
+            QtCore.QRectF(0, 0, self.fixed_width-10, self.height()))
 
         self.histogram_view.resize(self.fixed_width, self.height())
         self.histogram_view.setMouseTracking(True)
         self.histogram_view.viewport().installEventFilter(self)
 
-        self.density = QLineSeries()
         self.slider_density = int(self.height() / 3)
 
         # Create sliders
@@ -85,6 +78,7 @@ def __init__(self, width=50):
             self.sliders.append(self.slider_bars[-1])
         self.histogram.addSeries(self.sliders)
         self.histogram.zoom(2)  # at default zoom bars don't fill the chart
+        self.histogram.addSeries(self.density)
 
         # Layout
         self.layout = QGridLayout()
@@ -96,8 +90,6 @@ def __init__(self, width=50):
         self.bottom = 0
 
         # Get the values for window and level from the dict
-        patient_dict_container = PatientDictContainer()
-        print(patient_dict_container.get("dict_windowing"))  # testing
         windowing_limits = patient_dict_container.get("dict_windowing")['Normal']
 
         # Set window and level to the new values
@@ -114,8 +106,9 @@ def __init__(self, width=50):
         self.drag_upper_offset = 0
         self.drag_lower_offset = 0
 
-        # Test
-        self.set_density_histogram(gen_random_histogram())
+        # Generate the histogram
+        self.initialise_density_histogram()
+        self.update_density_histogram()
 
     def set_action_handler(self, action_handler):
         """
@@ -125,9 +118,14 @@ def set_action_handler(self, action_handler):
         """
         self.action_handler = action_handler
 
+    def set_dicom_view(self, dicom_view):
+        self.dicom_view = dicom_view
+        self.slice_slider = dicom_view.slider
+        self.dicom_view.windowing_slider = self
+
     def resizeEvent(self, event):
         self.histogram.setPlotArea(
-            QtCore.QRectF(0, 0, self.fixed_width, event.size().height()))
+            QtCore.QRectF(0, 0, self.fixed_width-10, event.size().height()))
 
     def height_to_index(self, pos):
         """
@@ -179,12 +177,49 @@ def set_density_histogram(self, densities):
         Index 0 is for the lowest density.
         :param densities: a list of values from 0-1
         """
-
+        self.histogram.removeSeries(self.density)
+        self.density = QLineSeries()
         self.density.setColor("grey")
         for i in range(0, len(densities)):
             self.density.append(2-densities[i], i)
         self.histogram.addSeries(self.density)
 
+    def update_density_histogram(self):
+        """
+        Updates the histogram display.
+        """
+        slice_index = self.slice_slider.value()
+        histogram_values = self.densities[slice_index]
+        self.set_density_histogram(histogram_values)
+
+    def initialise_density_histogram(self):
+        """
+        Initialises the density histograms.
+        """
+        slices = len(self.pixel_values)
+        self.densities = [[]] * slices
+        for s in range(slices):
+            self.densities[s] = [0] * WindowingSlider.MAX_PIXEL_VALUE
+
+            # Count each pixel value
+            pixels_flat = np.array(self.pixel_values[s]).flat
+            for pixel in pixels_flat:
+                # Clamp value between 0 and MAX_PIXEL_VALUE
+                p = min(pixel, WindowingSlider.MAX_PIXEL_VALUE)
+                p = max(p, 0)
+                p = round(p)
+                self.densities[s][p] += 1
+            max_value = max(self.densities[s])
+            min_value = min(self.densities[s])
+            avg_value = np.average(self.densities[s])
+
+            # Normalise values
+            for i in range(WindowingSlider.MAX_PIXEL_VALUE):
+                self.densities[s][i] = self.densities[s][i] / max_value * 10000
+                self.densities[s][i] = min(self.densities[s][i], 1)
+                self.densities[s][i] = max(self.densities[s][i], 0)
+        self.update_density_histogram()
+
     def update_bar(self, index, top_bar=True):
         """
         Moves the chosen bar to the provided index.