removed DoseSummationType handling, because I do not understand what …

…it means exactly. See comments. Cleanup up filestruc a bit, and allow gui to run without tpsdose

.gitignore

@@ -1,4 +1,4 @@
 __pycache__
-GPUMonteCarloDoseLibrary.dll
+dll/*.dll
 .vscode
-*.lnk
+*.lnk

README.md

@@ -16,14 +16,16 @@ Files in the root are executable scripts, subdirectories are libraries. The `dat
 
 `dicom` contains a small helper class to quickly get relevant data from a dicom file, and a function that helps you loop the dose engine over large quantities of treatments.
 
-`dll` contains some dlls required to run GPUMCD, including the wrapper dll that I provide to you without source code, because at this time I am not 100% sure I can license it the same as this repo. All files here are provided as a courtesy and are excluded from the license of this repo.
+`dll` is empty, and needs to be populated with some dlls by you. See `dll/placeholder.txt`. I do not redistribute them because I am not sure that I can.
 
 Installation
 ------------
 
 Right now, you must install the dependencies yourself.
 
-    $ pip(3) install medimage pyqt5
+    $ pip3 install medimage pyqt5
+
+Then, populated the `dll` directory to wherever pip installed the package, or, if checkout the git repo, in that directory. Alternatively, copy `dosia.ini`,`data` and `dll` from here, put it somewhere, and make sure you instantiate the Settings-object with this directory.
 
 This repo does NOT include GPUMCD, as this is not freely available software. You need to obtain GPUMCD from Elekta, in the form of a file called `GPUMonteCarloDoseLibrary.dll`, which could be provided to you as part of the Monaco treatment planning software, typically installed to `C:\Program Files\CMS\Monaco`. Right now, this file must be copied and placed in the `dll` subdir of this project.
 

dicom/__init__.py

@@ -40,7 +40,7 @@ def __init__(self,fname):
 			print(self.DoseSummationType)
 			assert self.DoseUnits == "GY", "This dose image is not in GY units."
 			assert self.DoseType == "PHYSICAL", "This dose image is not physical dose."
-			assert self.DoseSummationType in ["PLAN","FRACTION"], "This dose image is not per plan or fraction."
+			# assert self.DoseSummationType in ["PLAN","FRACTION"], "This dose image is not per plan or fraction."
 		elif self.modality == "RTPLAN":
 			self.sopid = str(self.data.SOPInstanceUID)
 			self.PatientPosition = str(self.data.PatientSetupSequence[0].PatientPosition)

dll/placeholder.txt

@@ -0,0 +1,8 @@
+The files that you should copy here are:
+
+* cudart64_80.dll
+* curand64_80.dll
+* msvcp120.dll (possibly)
+* msvcr120.dll (possibly)
+* libgpumcd.dll
+* GPUMonteCarloDoseLibrary.dll

gpumcd/__init__.py

@@ -42,23 +42,23 @@ def __init__(self,sett,ct,plan,plandose):
 			eng.get_dose(self.gpumcd_dose[-1])
 
 		for d in self.gpumcd_dose:
+			# If I look at dicompyler code, at no point do I see conditionals for multiplying with NumberOfFractionsPlanned. Therefore, below logic is commented out for now.
 			d.mul(plan.NumberOfFractionsPlanned)
 
-			#If I look at dicompyler code, at no point do I see conditionals for multiplying with NumberOfFractionsPlanned. 
-			if gpumcd_factor:
-					d.mul(plan.NumberOfFractionsPlanned)
-			else:
-				# From what I've seen, dosemaps are exported per plan REGARDLESS of value of DoseSummationType. we try anyway.
-				# https://dicom.innolitics.com/ciods/rt-dose/rt-dose/3004000a
-				if str(plandose.DoseSummationType).upper() == 'PLAN':
-					print("Dose was computed for whole PLAN, multiplying GPUMCD dose with number of fractions.")
-					d.mul(plan.NumberOfFractionsPlanned)
-				elif str(plandose.DoseSummationType).upper() == 'FRACTION':
-					#Editors note: 'FRACTION' here refers to fraction-GROUP-SEQUENCE! There may be multiple in a plan (and thus in a dose), altough I've never seen it. I could not find a defintion of 'fraction-group'. However, it does not correspond to what we call a fraction at the AvL: that's a session in DICOM parlance.
-					print("Dose was computed for FRACTION (-group!), multiplying GPUMCD dose with number of fractions.")
-					d.mul(plan.NumberOfFractionsPlanned)
-				elif str(plandose.DoseSummationType).upper() == 'BEAM':
-				else:
-					assert plandose.DoseSummationType == 'FRACTION'
+			# if gpumcd_factor:
+			# 		d.mul(plan.NumberOfFractionsPlanned)
+			# else:
+			# 	# From what I've seen, dosemaps are exported per plan REGARDLESS of value of DoseSummationType. we try anyway.
+			# 	# https://dicom.innolitics.com/ciods/rt-dose/rt-dose/3004000a
+			# 	if str(plandose.DoseSummationType).upper() == 'PLAN':
+			# 		print("Dose was computed for whole PLAN, multiplying GPUMCD dose with number of fractions.")
+			# 		d.mul(plan.NumberOfFractionsPlanned)
+			# 	elif str(plandose.DoseSummationType).upper() == 'FRACTION':
+			# 		#Editors note: 'FRACTION' here refers to fraction-GROUP-SEQUENCE! There may be multiple in a plan (and thus in a dose), altough I've never seen it. I could not find a defintion of 'fraction-group'. However, it does not correspond to what we call a fraction at the AvL: that's a session in DICOM parlance.
+			# 		print("Dose was computed for FRACTION (-group!), multiplying GPUMCD dose with number of fractions.")
+			# 		d.mul(plan.NumberOfFractionsPlanned)
+			# 	elif str(plandose.DoseSummationType).upper() == 'BEAM':
+			# 	else:
+			# 		assert plandose.DoseSummationType == 'FRACTION'
 
 		# self.gpumcd_dose = ct_obj.dosemap

gpumcd/settings.py

@@ -11,7 +11,7 @@ def __init__(self,dosia_ini_dir=None):
 		defkwargs = {
 			'directories':{ # relative to dosia.ini or absolute
 				'material_data': path.join(dosia_ini_dir,'data/materials_clin'),
-				'gpumcd_dll': path.join(dosia_ini_dir,'data/dll'),
+				'gpumcd_dll': path.join(dosia_ini_dir,'dll'),
 				'hounsfield_conversion': path.join(dosia_ini_dir,'data/hounsfield')
 			},
 			'gpumcd_machines':{
@@ -77,7 +77,7 @@ def __init__(self,dosia_ini_dir=None):
 			if path.isdir("C:/Program Files/CMS/Monaco"):
 				self.directories['gpumcd_dll'] = "C:/Program Files/CMS/Monaco"
 				from shutil import copyfile
-				copyfile(path.join(dosia_ini_dir,'data/dll/libgpumcd.dll'),self.directories['gpumcd_dll'])
+				copyfile(path.join(dosia_ini_dir,'dll/libgpumcd.dll'),self.directories['gpumcd_dll'])
 			else:
 				self.directories['gpumcd_dll'] = cfg.get('directories','gpumcd_dll').replace('\\','/')
 			assert(path.isdir(self.directories['gpumcd_dll']))

gui.py

@@ -111,7 +111,7 @@ def __init__(self, *args,**kwargs):
 
 	def resetpanes(self):
 		try:
-			if self.planpane.ready and self.plandosepane.ready and self.ctpane.ready:
+			if self.planpane.ready and self.ctpane.ready: #no plandoseready
 				self.menu_gpumcd_calculate.setDisabled(False)
 				# self.menu_gpumcd_setmachfile.setDisabled(False)
 		except:
@@ -166,7 +166,14 @@ def setmachfilegpumcd(self):
 		self.planpane.plan.accelerator.setmachfile(machfile)
 
 	def calcgpumcd(self):
-		dosia = gpumcd.Dosia(self.sett,self.ctpane.image[0],self.planpane.plan,self.plandosepane.image[0])
+		try:
+			self.plandosepane.ready
+			dosia = gpumcd.Dosia(self.sett,self.ctpane.image[0],self.planpane.plan,self.plandosepane.image[0])
+		except:
+			c = self.ctpane.image[0].copy()
+			c.resample([3,3,3])
+			c.zero_out()
+			dosia = gpumcd.Dosia(self.sett,self.ctpane.image[0],self.planpane.plan,c)
 
 		self.gpumcdpane = ImagePane(dosia.gpumcd_dose) #FIXME: prepare for sum_beams = False
 		self.menu_gpumcd_save.setDisabled(False)