Merge mammo 20260416

gecatsim/clib_build/src/analytic_projector.h

@@ -27,7 +27,7 @@ int n_row_oversample = 1;
 int n_col_oversample_add_xtalk = 1;
 int n_row_oversample_add_xtalk = 1;
 
-struct module_info
+struct analytic_module_info
 {
   double *Height;
   double *Width;
@@ -43,7 +43,7 @@ struct module_info
   int moduleOverlapType;
 };
 
-struct module_info modules = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0,0};
+struct analytic_module_info analytic_modules = {NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0,0};
 
 struct pnt
 {
@@ -61,7 +61,7 @@ struct bounding_info
 
 struct bounding_info bounding = {NULL,NULL};
 
-struct phantom_info
+struct analytic_phantom_info
 {
   int numObjects;
   int *objectType;
@@ -77,7 +77,7 @@ struct phantom_info
   double xbounds[2];
 };
 
-struct phantom_info phantom = {0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,{0,0}};
+struct analytic_phantom_info analytic_phantom = {0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,{0,0}};
 
 struct material_info
 {
@@ -86,7 +86,7 @@ struct material_info
   double *muTable;
 };
 
-struct material_info materials = {0,0,NULL};
+struct material_info analytic_materials = {0,0,NULL};
 
 struct projector_args
 {

gecatsim/clib_build/src/phantom.tab.cpp

@@ -64,7 +64,7 @@
 typedef struct phantomlval {
   double val;
   double vec[3];
-  char str[128];
+  char str[2048];
 } PHANTOMLVAL;
 
 #endif
@@ -290,7 +290,7 @@ typedef struct phantomlval {
 typedef union YYSTYPE {
   double val;
   double vec[3];
-  char str[128];
+  char str[2048];
 } YYSTYPE;
 /* Line 191 of yacc.c.  */
 //#line 283 "phantom.tab.cpp"

gecatsim/clib_build/src/phantom.tab.hpp

@@ -110,7 +110,7 @@
 typedef union YYSTYPE {
   double val;
   double vec[3];
-  char str[128];
+  char str[2048];
 } YYSTYPE;
 /* Line 1275 of yacc.c.  */
 #line 113 "phantom.tab.hpp"

gecatsim/pyfiles/C_Projector_SetData.py

@@ -31,6 +31,8 @@ def C_Projector_SetData(cfg, viewId, subViewId):
 def get_projector_id(cfg):
     if not isinstance(cfg.phantom.callback, list):
         phantom_callbacks = [cfg.phantom.callback]
+    elif isinstance(cfg.phantom.callback, list) and isinstance(cfg.phantom.callback[0], list):
+        phantom_callbacks = cfg.phantom.callback[cfg.viewId]
     else:
         phantom_callbacks = cfg.phantom.callback
     projectorIDs = []

gecatsim/pyfiles/C_Projector_Voxelized.py

@@ -51,7 +51,8 @@ def C_Projector_Voxelized(cfg, viewId, subViewId):
             unused7 = 7
             freeTheMemory = 0
 
-            if viewId==cfg.sim.stopViewId and subViewId==cfg.sim.subViewCount-1 \
+            # ZJY recalcPht is helpful in reducing memory usage in dynamic phantom
+            if (cfg.physics.recalcPht or (viewId==cfg.sim.stopViewId and subViewId==cfg.sim.subViewCount-1))\
                 and srcId==src.nSamples-1 and matId==cfg.phantom.numberOfMaterials-1:
                 freeTheMemory = 1
 

gecatsim/pyfiles/CommonTools.py

@@ -26,11 +26,12 @@ def make_col(a):
     return a
 
 
-def feval(func_name, *args):
+def feval(funcName, *args):
     module_paths = [
-        func_name,
-        f"gecatsim.pyfiles.{func_name}",
-        f"gecatsim.pyfiles.FlatPanel.{func_name}"
+        funcName,
+        f"gecatsim.pyfiles.{funcName}",
+        f"gecatsim.pyfiles.FlatPanel.{funcName}",
+        f"gecatsim.src.app.pyfiles.{funcName}"
     ]
 
     module = None
@@ -42,15 +43,15 @@ def feval(func_name, *args):
             continue
 
     if module is None:
-        raise ImportError(f"Could not import module: {func_name}. Tried paths: {module_paths}")
+        raise ImportError(f"Could not import module: {funcName}. Tried paths: {module_paths}")
 
     # Extract the function name (the part after the last dot)
-    func_name_only = func_name.split('.')[-1]
+    funcName_only = funcName.split('.')[-1]
 
     try:
-        func = getattr(module, func_name_only)
+        func = getattr(module, funcName_only)
     except AttributeError:
-        raise AttributeError(f"Function '{func_name_only}' not found in module '{module.__name__}'")
+        raise AttributeError(f"Function '{funcName_only}' not found in module '{module.__name__}'")
 
     return func(*args)
 
@@ -74,16 +75,35 @@ def load_C_lib():
 
 
 class emptyCFG:
-    pass
+
+    def __str__(self):
+        attrs = ', '.join(f"{key}={value!r}" for key, value in self.__dict__.items())
+        return f"{self.__class__.__name__}({attrs})"
+
+    def __repr__(self):
+        return self.__str__()
+
+
 
+import sys
 
 class PathHelper:
     def __init__(self):
         self._base_dir = os.getcwd()
         # Locate paths of lib and data.
         self.paths = {}
-        self.paths["main"] = os.path.dirname(os.path.abspath(__file__))
-        self.paths["top"] = os.path.split(self.paths["main"])[0]
+
+        # Handle PyInstaller bundled environment
+        if getattr(sys, 'frozen', False) and hasattr(sys, '_MEIPASS'):
+            # Running as compiled executable
+            bundle_dir = sys._MEIPASS
+            self.paths["main"] = os.path.join(bundle_dir, 'app', 'pyfiles')
+            self.paths["top"] = os.path.join(bundle_dir, 'app')
+        else:
+            # Running as normal Python script
+            self.paths["main"] = os.path.dirname(os.path.abspath(__file__))
+            self.paths["top"] = os.path.split(self.paths["main"])[0]
+
         self.paths["bowtie"] = os.path.join(self.paths["top"], 'bowtie')
         self.paths["cfg"] = os.path.join(self.paths["top"], 'cfg')
         self.paths["dose"] = os.path.join(self.paths["top"], 'dose')
@@ -259,7 +279,6 @@ def source_cfg(*para):
 
     # initialize structs in cfg and structs
     attrList = ['sim', 'det', 'detNew', 'src', 'srcNew', 'spec', 'protocol', 'scanner', 'phantom', 'physics', 'recon', 'dose']
-
     for attr in attrList:
         # Ensure cfg has the attribute
         if not hasattr(cfg, attr):
@@ -381,27 +400,60 @@ def overlap2d(oldimg, old_pos_x, old_pos_y, pos_x, pos_y):
 def rawread(fname, dataShape, dataType):
     # dataType is for numpy, ONLY allows: 'float'/'single', 'double', 'int'/'int32', 'uint'/'uint32', 'int8', 'int16' 
     #          they are single, double, int32, uin32, int8, int16
-    with open(fname, 'rb') as fin:
-        data = fin.read()
-
     # https://docs.python.org/3/library/struct.html
-    switcher = {'float': ['f', 4, np.single], 
-                'single': ['f', 4, np.single], 
-                'double': ['d', 8, np.double], 
+    switcher = {'float': ['f', 4, np.float32], 
+                'float32': ['f', 4, np.float32],
+                'single': ['f', 4, np.float32], 
+                'double': ['d', 8, np.float64], 
                 'int': ['i', 4, np.int32], 
                 'uint': ['I', 4, np.uint32],  
                 'int32': ['i', 4, np.int32], 
                 'uint32': ['I', 4, np.uint32], 
+                'uint8': ['B', 1, np.uint8],
                 'int8': ['b', 1, np.int8], 
                 'int16': ['h', 2, np.int16]}
-    fmt = switcher[dataType]
-    data = struct.unpack("%d%s" % (len(data)/fmt[1], fmt[0]), data)
 
-    data = np.array(data, dtype=fmt[2])
+    fmt_char, byte_size, np_dtype = switcher[dataType]
+
+    # Use numpy.fromfile for direct binary reading - much faster
+    try:
+        data = np.fromfile(fname, dtype=np_dtype)
+    except:
+        # Fallback to manual reading if fromfile fails
+        with open(fname, 'rb') as fin:
+            raw_data = fin.read()
+        num_elements = len(raw_data) // byte_size
+        data = struct.unpack(f"{num_elements}{fmt_char}", raw_data)
+        data = np.array(data, dtype=np_dtype)
+
     if dataShape:
         data = data.reshape(dataShape)
 
     return data
+
+    # with open(fname, 'rb') as fin:
+    #     data = fin.read()
+
+    # # https://docs.python.org/3/library/struct.html
+    # switcher = {'float': ['f', 4, np.single], 
+    #             'float32': ['f', 4, np.float32],
+    #             'single': ['f', 4, np.single], 
+    #             'double': ['d', 8, np.double], 
+    #             'int': ['i', 4, np.int32], 
+    #             'uint': ['I', 4, np.uint32],  
+    #             'int32': ['i', 4, np.int32], 
+    #             'uint32': ['I', 4, np.uint32], 
+    #             'uint8': ['B', 1, np.uint8],
+    #             'int8': ['b', 1, np.int8], 
+    #             'int16': ['h', 2, np.int16]}
+    # fmt = switcher[dataType]
+    # data = struct.unpack("%d%s" % (len(data)/fmt[1], fmt[0]), data)
+
+    # data = np.array(data, dtype=fmt[2])
+    # if dataShape:
+    #     data = data.reshape(dataShape)
+
+    # return data
 
 def rawwrite(fname, data):
     with open(fname, 'wb') as fout:

gecatsim/pyfiles/Detector_RayAngles_2D.py

@@ -30,7 +30,7 @@ def Detector_RayAngles_2D(cfg):
 
         xyzDet = nm.repmat(det.modCoords[m, :], nCells, 1) + \
             det.cellCoords @ (np.c_[det.uvecs[m, :], det.vvecs[m, :]].T)
-        xyzR = xyzDet - nm.repmat(xyzSrc, nCells, 1);
+        xyzR = xyzDet - nm.repmat(xyzSrc, nCells, 1)
 
         cellInd = range(startInd, startInd+nCells)
         rayDistance[cellInd] = vectornorm(xyzR.T)