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ENH: Orthovoltage dose engine execution
- ctcreate generation fixed and validated; Output handled and logged - DICOM to DOSXYZnrc beam angle conversion function added; Added EGSnrcUtil.py containing common EGSnrc methods not specific to the orthovoltage use case - DOSXYZnrc input parameters fixed - DOSXZYnrc execution Re #73
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| import os | ||
| import vtk, qt, ctk, slicer | ||
| import logging | ||
|
|
||
| #------------------------------------------------------------------------------ | ||
| # | ||
| # EGSnrcUtil | ||
| # | ||
| # Common utility functions for using EGSnrc (DOSXYZnrc) based dose engines | ||
| # from SlicerRT. | ||
| # | ||
| #------------------------------------------------------------------------------ | ||
|
|
||
| #----------------------------------------------------------------------------- | ||
| def generateSlicenamesTextfile(ctDicomSeriesUID, slicenamesFilename, outputFolder): | ||
| """ Generate slicenames.txt file, with list of ct dicom slices, in increasing slice order (IS direction) | ||
| """ | ||
| filePaths = slicer.dicomDatabase.filesForSeries(ctDicomSeriesUID) | ||
| if len(filePaths) == 0: | ||
| logging.error('Failed to find files in DICOM database for UID ' + str(ctDicomSeriesUID)) | ||
| return False | ||
|
|
||
| from DICOMLib import DICOMUtils | ||
| unsortedFileList = slicer.dicomDatabase.filesForSeries(ctDicomSeriesUID) | ||
| sortedFileList, distances, warnings = DICOMUtils.getSortedImageFiles(unsortedFileList) | ||
|
|
||
| outFile = open(os.path.join(outputFolder, slicenamesFilename), "w") | ||
| counter = 1 | ||
| numDicomFiles = len(sortedFileList) | ||
| for sliceFileName in sortedFileList: | ||
| outFile.write(sliceFileName) | ||
| if counter != numDicomFiles: | ||
| outFile.write("\n") | ||
| counter += 1 | ||
| outFile.close() | ||
| return True | ||
|
|
||
| #----------------------------------------------------------------------------- | ||
| def callCtcreate(ctcreateExecFilePath, outputFolder, ctcreateInputFilename="ctcreate.inp"): | ||
| """ Call ctcreate executable. Use this function after generating input for ctcreate | ||
| """ | ||
| # If egsphant file exists, remove it | ||
| outputCtcreatePhantomPath = os.path.join(outputFolder, "slicenames.txt.egsphant") | ||
| if os.path.exists(outputCtcreatePhantomPath): | ||
| logging.warning("Ctcreate phantom already exists in specifying directory. Overwriting it...") | ||
| os.remove(outputCtcreatePhantomPath) | ||
|
|
||
| # User must have ctcreate installed | ||
| ctcreateInputFilePath = os.path.join(outputFolder, ctcreateInputFilename) | ||
| logging.info("Run ctcreate: " + ctcreateExecFilePath + ' ' + ctcreateInputFilePath) | ||
|
|
||
| import subprocess | ||
| proc = subprocess.Popen([ctcreateExecFilePath, ctcreateInputFilePath], stdout=subprocess.PIPE, shell=True) | ||
| (out, err) = proc.communicate() | ||
|
|
||
| outStr = str(out).replace('\\r','').replace('\\n','\n') | ||
| logging.debug("ctcreate output: \n" + outStr) | ||
| outStr = outStr[:outStr.rfind("'")] # Strip closing single quote | ||
| if outStr[len(outStr)-1:] == '\n': | ||
| outStr = outStr[:len(outStr)-1] # Strip last empty line if any | ||
| logging.info("ctcreate output (last paragraph): \n" + outStr[outStr.rfind('\n\n')+2:]) | ||
| if err is not None and str(err) != '': | ||
| logging.error("ctcreate error: \n" + str(err)) | ||
|
|
||
| #----------------------------------------------------------------------------- | ||
| def dcm2dosxyz(AngleGantry, AngleCouch, AngleCollimator, Method='Zhan'): | ||
| """ | ||
| Coordinate transformation from DICOM to DOSXYZnrc | ||
| Input: gantry angle, couch angle and collimator angle from DICOM | ||
| Output: theta, phi, phicol for DOSXYZnrc (using BEAMnrc phsp) | ||
| The default method is what proposed in the article | ||
| Zhan, L., Jiang, R., & Osei, E. K. (2012). Beam coordinate transformations | ||
| from DICOM to DOSXYZnrc. Physics in Medicine & Biology, 57(24), N513. | ||
| Also provided are the implementations based on Thebaut's and Bush's methods | ||
| for readers' convenience. The authors assume no guarantee that these | ||
| are the best implementations. | ||
| """ | ||
| import numpy as np | ||
| gamma = AngleGantry*np.pi/180.0 | ||
| col = AngleCollimator*np.pi/180.0 | ||
| rho = AngleCouch*np.pi/180 | ||
| # distort Couch and Gantry angles slightly to avoid | ||
| # very special cases | ||
| if AngleCouch in (90.0,270.0) and AngleGantry in (90.0,270.0): | ||
| rho = rho * 0.999999 | ||
| gamma = gamma * 0.999999 | ||
| if Method=='Zhan': # this paper | ||
| sgsr = np.sin(gamma)*np.sin(rho) | ||
| sgcr = np.sin(gamma)*np.cos(rho) | ||
| theta = np.arccos(-sgsr) | ||
| phi = np.arctan2(-np.cos(gamma),sgcr) | ||
| CouchAngle2CollPlane = np.arctan2(-np.sin(rho)*np.cos(gamma), np.cos(rho)) | ||
| phicol = (col-np.pi/2) + CouchAngle2CollPlane | ||
| # coord. trans. for BEAMnrc generated phsp to DOSXYZnrc. | ||
| phicol = np.pi - phicol | ||
| elif Method=='Bush': # Bush, Australas. Phys. Eng. Sci. | ||
| # (2010) 33:351 | ||
| rho = 2*np.pi-rho | ||
| sgsr = np.sin(gamma)*np.sin(rho) | ||
| sgcr = np.sin(gamma)*np.cos(rho) | ||
| cgsr = np.cos(gamma)*np.sin(rho) | ||
| theta = np.arctan2(np.sqrt(1.0-sgsr**2),sgsr) | ||
| phi = np.arctan2(-np.cos(gamma),sgcr) | ||
| col = col - np.pi/2 | ||
| phicol = np.arctan2( (-cgsr*np.cos(col)-np.cos(rho)*np.sin(col)), | ||
| (cgsr*np.sin(col)-np.cos(rho)*np.cos(col)) ) | ||
| phicol = 2*np.pi-phicol | ||
| elif Method=='Thebaut': # Thebaut, Phys. Med. Biol. (2006) 51:N441 | ||
| rho = 2*np.pi-rho | ||
| sgsr = np.sin(gamma)*np.sin(rho) | ||
| sgcr = np.sin(gamma)*np.cos(rho) | ||
| cgcr = np.cos(gamma)*np.cos(rho) | ||
| theta = np.arccos(sgsr) | ||
| phi = np.arctan2(-np.cos(gamma),sgcr) | ||
| col = col - np.pi/2 | ||
| cos_phicol = np.cos(col)*cgcr*np.sin(phi) - \ | ||
| np.sin(col)*np.sin(rho)*np.sin(phi) - \ | ||
| np.cos(col)*np.sin(gamma)*np.cos(phi) | ||
| if cos_phicol>1.0: # for possible binary express problem. | ||
| cos_phicol = 1.0 | ||
| elif cos_phicol<-1.0: | ||
| cos_phicol = -1.0 | ||
| phicol = np.arccos(cos_phicol) # return value within [0,pi] | ||
| direct = np.cos(col)*np.sin(rho)*np.sin(phi) + \ | ||
| np.sin(col)*(cgcr*np.sin(phi)- \ | ||
| np.sin(gamma)*np.cos(phi)) | ||
| if direct>0: | ||
| phicol = -np.abs(phicol) | ||
| else: | ||
| phicol = np.abs(phicol) | ||
| else: | ||
| logging.error('Incorrect c.s. transformation method') | ||
| return None | ||
|
|
||
| return (theta*180/np.pi, np.mod(phi*180/np.pi,360), \ | ||
| np.mod(phicol*180/np.pi,360)) |
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