Add CatPhan604

.checkignore

@@ -1,2 +1,8 @@
-# Ignore test folder
-tests/*
+# Ignore folders
+tests/*
+env/*
+demo_files/*
+__pycache__/*
+
+# Ignore files
+*.old

.gitignore

@@ -0,0 +1,10 @@
+# Folders to ignore
+env/*
+tests/*
+**/pylinac.egg-info
+**/demo_files
+**/__pycache__
+
+#Files to ignore
+*.old
+.directory

pylinac/__init__.py

@@ -9,7 +9,7 @@
     raise ValueError("Pylinac is only supported on Python 3.x. It seems you are using Python 2; please use a different interpreter.")
 
 # import shortcuts
-from pylinac.ct import CatPhan504, CatPhan600, CatPhan503
+from pylinac.ct import CatPhan504, CatPhan600, CatPhan503, CatPhan604
 from pylinac.core import decorators, geometry, image, io, mask, profile, roi, utilities
 from pylinac.core.utilities import clear_data_files, assign2machine
 from pylinac.flatsym import BeamImage

pylinac/ct.py

@@ -213,8 +213,8 @@ def phan_center(self):
 class CatPhanModule(Slice, ROIManagerMixin):
     """Base class for a CTP module.
     """
-    combine_method = 'mean'
-    num_slices = 0
+    combine_method = 'max'
+    num_slices = 1
 
     def __init__(self, catphan, tolerance, offset=0):
         """
@@ -308,6 +308,23 @@ def __init__(self, catphan, offset, hu_tolerance, thickness_tolerance, scaling_t
                 },
                 'background ROI angles': [-30, -150, -210, 30]
             }
+        elif isinstance(catphan, CatPhan604):
+            self.hu = {
+                'distance to ROIs': 58.7/self.mm_per_pixel,
+                'ROI radius': 5/self.mm_per_pixel,
+                'ROIs': {
+                    'Air': {'value': -1000, 'angle': -90},
+                    'PMP': {'value': -200, 'angle': -120},
+                    '50Bone': {'value': 725, 'angle': -150},
+                    'LDPE': {'value': -100, 'angle': 180},
+                    'Poly': {'value': -35, 'angle': 120},
+                    'Acrylic': {'value': 120, 'angle': 60},
+                    '20Bone': {'value': 240, 'angle': 30},
+                    'Delrin': {'value': 340, 'angle': 0},
+                    'Teflon': {'value': 990, 'angle': -60},
+                },
+                'background ROI angles': [-30, -210]
+            }
         self.bg_hu_rois = OrderedDict()
         self.hu_rois = OrderedDict()
 
@@ -633,6 +650,9 @@ def preprocess(self, catphan):
         elif isinstance(catphan, CatPhan600):
             self.start_angle = np.pi - 0.1
             self.ccw = False
+        elif isinstance(catphan, CatPhan604):
+            self.start_angle = np.pi
+            self.ccw = True
 
     @property
     @lru_cache(maxsize=1)
@@ -1065,9 +1085,9 @@ def find_origin_slice(self):
             The middle slice of the HU linearity module.
         """
         hu_slices = []
-        for image_number in range(0, self.num_images, 2):
+        for image_number in range(0, self.num_images):
             slice = Slice(self, image_number, combine=False)
-            # print(image_number)
+            #print(image_number)
             # slice.image.plot()
             try:
                 center = slice.phan_center
@@ -1079,9 +1099,10 @@ def find_origin_slice(self):
                 # determine if the profile contains both low and high values and that most values are the same
                 low_end, high_end = np.percentile(prof, [2, 98])
                 median = np.median(prof)
-                if (low_end < median - 400) and (high_end > median + 400) and (
+                if (low_end < median - 800) and (high_end > median + 800) and (
                                 np.percentile(prof, 80) - np.percentile(prof, 20) < 100):
                     hu_slices.append(image_number)
+                    #print(image_number)
 
         if not hu_slices:
             raise ValueError("No slices were found that resembled the HU linearity module")
@@ -1092,6 +1113,7 @@ def find_origin_slice(self):
         hu_slices = hu_slices[((c + ln/2) >= hu_slices) & (hu_slices >= (c - ln/2))]
         center_hu_slice = int(round(np.median(hu_slices)))
         if self._is_within_image_extent(center_hu_slice):
+            #print(center_hu_slice)
             return center_hu_slice
 
     @lru_cache(maxsize=1)
@@ -1325,7 +1347,7 @@ class CatPhan503(CatPhanBase):
     def run_demo(cls, show=True):
         """Run the CBCT demo using high-quality head protocol images."""
         obj = cls.from_demo_images()
-        obj.analyze()
+        obj.analyze()   
         print(obj.results())
         obj.plot_analyzed_image(show)
         # cbct = CatPhan503.from_demo_images()
@@ -1357,6 +1379,29 @@ def run_demo(show=True):
         cbct.plot_analyzed_image(show)
 
 
+class CatPhan604(CatPhanBase):
+    """A class for loading and analyzing CT DICOM files of a CatPhan 604. Can be from a CBCT or CT scanner
+    Analyzes: Uniformity (CTP486), High-Contrast Spatial Resolution (CTP528),
+    Image Scaling & HU Linearity (CTP404), and Low contrast (CTP515).
+    """
+    _demo_url = 'CatPhan604.zip'
+    _model = '604'
+    catphan_radius_mm = 101
+    modules = {
+        CTP486: {'offset': -80},
+        CTP528: {'offset': 40},
+        CTP515: {'offset': -40}
+    }
+
+    @staticmethod
+    def run_demo(show=True):
+        """Run the CBCT demo using high-quality head protocol images."""
+        cbct = CatPhan604.from_demo_images()
+        cbct.analyze()
+        print(cbct.results())
+        cbct.plot_analyzed_image(show)
+
+
 class CatPhan600(CatPhanBase):
     """A class for loading and analyzing CT DICOM files of a CatPhan 600.
     Analyzes: Uniformity (CTP486), High-Contrast Spatial Resolution (CTP528),

pylinac/py_gui.py

@@ -2,6 +2,7 @@
 from tkinter import *
 from tkinter.ttk import *
 from tkinter import filedialog
+from tkinter import messagebox
 import os.path as osp
 import webbrowser
 
@@ -403,7 +404,15 @@ def init_tg51(self):
 
 
 def gui():
+
+    def on_exit():
+        if messagebox.askokcancel("Quit", "Do you want to quit?"):
+            root.quit()
+
     root = Tk()
     root.title('Pylinac GUI ' + __version__)
+    root.protocol("WM_DELETE_WINDOW", on_exit)
     app = PylinacGUI(master=root)
     app.mainloop()
+    root.destroy()
+    del root