from __future__ import division import re,types,struct from libtbx.test_utils import approx_equal from scitbx.array_family import flex from iotbx.detectors.detectorbase import DetectorImageBase from iotbx.detectors import ReadDTrek verbose=False class DTREKImage(DetectorImageBase): """enforce dTREK Image Format v1.1, using Rigaku/MSC documentation.""" def __init__(self,filename): DetectorImageBase.__init__(self,filename) self.vendortype = "RAXIS" def read_vendor_header(self): G = open(self.filename, "rb") try: assert G.read(14)=="{\nHEADER_BYTES" raw = [charac for charac in G.read(6) if charac.isdigit()] header_bytes = int("".join(raw)) assert header_bytes%512==0 G.seek(0) padded_header = G.read(header_bytes) finally: # ensure that the file gets closed no matter what! G.close() unpadded_header = padded_header.rstrip() assert unpadded_header[0:2]=="{\n" assert unpadded_header[-2:]=="\n}" self.header = padded_header raw_key_values = unpadded_header[2:-3].split(";\n") self.headerlines = []; self.keys={} for i in raw_key_values: self.headerlines.append( i.split("=") ) self.keys[self.headerlines[-1][0]]=self.headerlines[-1][1] def enforce_types(self): # mandate:=( regex_expression, python_type, length ) # length:= 1: single variable # 0: unknown, could be multiple # >1: definite multiple value self.enf= [("SIZE1",int,1), ("SIZE2",int,1), ("SATURATED_VALUE",int,1), ("DETECTOR_NAMES",types.StringType,0), (r"\n([0-9A-Za-z]+_DETECTOR_DIMENSIONS)",float,2), (r"\n([0-9A-Za-z]+_DETECTOR_SIZE)",float,2), (r"\n(ROTATION)=",float,10), (r"\n([0-9A-Za-z]+_GONIO_NAMES)",types.StringType,0), (r"\n([0-9A-Za-z]+_GONIO_UNITS)",types.StringType,0), (r"\n([0-9A-Za-z]+_GONIO_VALUES)",float,0), ("SOURCE_WAVELENGTH",float,2), #must be one wavelength (r"\n([0-9A-Za-z]+_SPATIAL_DISTORTION_TYPE)",types.StringType,1), (r"\n([0-9A-Za-z]+_SPATIAL_DISTORTION_INFO)",float,4), ("DETECTOR_TYPE",types.StringType,1), ("DATA_TYPE",types.StringType,1), ("BYTE_ORDER",types.StringType,1), ("RAXIS_COMPRESSION_RATIO",int,1), ("HEADER_BYTES",int,1), ] for mandate in self.enf: pattern = re.compile(mandate[0]) matches = pattern.findall(self.header) for match in matches: if verbose: print match, if mandate[2]==1: self.keys[match] = mandate[1](self.keys[match]) else: all_tokens = self.tokenize(self.keys[match]) all_values = [mandate[1](az) for az in all_tokens] if mandate[2] > 1: assert len(all_values)==mandate[2] self.keys[match] = all_values if verbose: print self.keys[match], print for integer in ["SIZE1","SIZE2","SATURATED_VALUE"]: self.keys[integer]=int(self.keys[integer]) def tokenize(self,string_): if type(string_) is list: return string_ tokens = string_.split(" ") while "" in tokens: tokens.remove("") return tokens def generic_param_from_vendor_head(self): self.parameters={} if verbose: for i in self.headerlines: print "%29s"%i[0],self.keys[i[0]] # Note that SIZE1 is slow for ADSC/CBF but fast for RAXIS # Note that SIZE2 is fast for ADSC/CBF but slow for RAXIS self.parameters['SIZE1'] = self.keys["SIZE1"] self.parameters['SIZE2'] = self.keys["SIZE2"] self.parameters['CCD_IMAGE_SATURATION'] = self.keys["SATURATED_VALUE"] dname_prefix = self.keys["DETECTOR_NAMES"][0] sizes = flex.double(self.keys[dname_prefix+"DETECTOR_SIZE"]) pixels = flex.double(self.keys[dname_prefix+"DETECTOR_DIMENSIONS"]) pixel_sizes = sizes/pixels assert pixel_sizes[0]==pixel_sizes[1] self.parameters['PIXEL_SIZE'] = pixel_sizes[0] assert approx_equal(self.keys["ROTATION"][1]-self.keys["ROTATION"][0], self.keys["ROTATION"][2]) self.parameters['OSC_START'] = self.keys["ROTATION"][0] self.parameters['OSC_RANGE'] = self.keys["ROTATION"][2] distance_idx = self.keys[dname_prefix+"GONIO_NAMES"].index("Distance") assert self.keys[dname_prefix+"GONIO_UNITS"][distance_idx]=="mm" self.parameters['DISTANCE'] = self.keys[dname_prefix+"GONIO_VALUES"][distance_idx] assert self.keys["SOURCE_WAVELENGTH"][0]==1.0 self.parameters['WAVELENGTH'] = self.keys["SOURCE_WAVELENGTH"][1] assert self.keys[dname_prefix+"SPATIAL_DISTORTION_TYPE"]=="Simple_spatial" check_pixel_sizes = flex.double( self.keys[dname_prefix+"SPATIAL_DISTORTION_INFO"][2:4]) assert check_pixel_sizes == pixel_sizes beam_mm = flex.double( self.keys[dname_prefix+"SPATIAL_DISTORTION_INFO"][0:2])*pixel_sizes self.parameters['BEAM_CENTER_X'] = beam_mm[0] self.parameters['BEAM_CENTER_Y'] = beam_mm[1] tt_idx = self.keys[dname_prefix+"GONIO_NAMES"].index("2Theta") assert self.keys[dname_prefix+"GONIO_UNITS"][tt_idx]=="deg" self.parameters['TWOTHETA'] = self.keys[dname_prefix+"GONIO_VALUES"][tt_idx] if self.keys.has_key("DETECTOR_TYPE"): self.parameters['DETECTOR_SN'] = self.keys["DETECTOR_TYPE"] elif self.keys.has_key(self.keys["DETECTOR_NAMES"][0] + "DETECTOR_IDENTIFICATION"): self.parameters['DETECTOR_SN'] = self.keys[self.keys["DETECTOR_NAMES"][0] + "DETECTOR_IDENTIFICATION"] else: self.parameters['DETECTOR_SN'] = "No serial number" def readHeader(self,): if not self.parameters: self.read_vendor_header() self.enforce_types() self.generic_param_from_vendor_head() def getEndian(self): self.readHeader() if self.keys['BYTE_ORDER'].lower().find('big')>=0: return 1 #big_endian else: return 0 #little_endian def read(self): G = open(self.filename, "rb") try: G.seek(self.keys["HEADER_BYTES"]) endian_code = {'little_endian':'<','big_endian':'>'}[self.keys["BYTE_ORDER"]] type_code = {'signed char':'b', 'unsigned char':'B', 'short int':'h', 'long int':'i', 'unsigned short int':'H', 'unsigned long int':'I', 'float IEEE':'f', }[self.keys['Data_type']] type_size = {'b':1,'B':1,'h':2,'H':2,'i':4,'I':4,'f':4}[type_code] assert not type_code=="I" # for I, a flex.int() will exceed type limits array_size = self.parameters['SIZE1'] * self.parameters['SIZE2'] rawdata = G.read(array_size * type_size) finally: # ensure that the file gets closed no matter what! G.close() #Python prototype-- #doesn't handle raxis uncompression & is 10x slower than C++ version #uncoded_data = struct.unpack(endian_code+type_code*array_size,rawdata) #provisional_data = flex.int(uncoded_data) #provisional_data.reshape(flex.grid((self.parameters['SIZE2'], # self.parameters['SIZE1']))) #self.bin_safe_set_data(provisional_data) self.bin_safe_set_data( ReadDTrek(raw=rawdata,type_code=type_code, slow=self.parameters['SIZE2'], fast=self.parameters['SIZE1'], swap=self.endian_swap_required(), uncompress=self.keys.get("RAXIS_COMPRESSION_RATIO",1) ))