def run(self, rinput): self.logger.info('starting processing for bars detection') flow = self.init_filters(rinput) hdulist = basic_processing_with_combination(rinput, flow=flow) hdr = hdulist[0].header self.set_base_headers(hdr) self.save_intermediate_img(hdulist, 'reduced_image.fits') try: rotang = hdr['ROTANG'] tsutc1 = hdr['TSUTC1'] dtub, dtur = datamodel.get_dtur_from_header(hdr) csupos = datamodel.get_csup_from_header(hdr) if len(csupos) != 2 * EMIR_NBARS: raise RecipeError('Number of CSUPOS != 2 * NBARS') csusens = datamodel.get_cs_from_header(hdr) except KeyError as error: self.logger.error(error) raise RecipeError(error) self.logger.debug('start finding bars') allpos, slits = find_bars( hdulist, rinput.bars_nominal_positions, csupos, dtur, average_box_row_size=rinput.average_box_row_size, average_box_col_size=rinput.average_box_col_size, fit_peak_npoints=rinput.fit_peak_npoints, median_filter_size=rinput.median_filter_size, logger=self.logger) self.logger.debug('end finding bars') if self.intermediate_results: with open('ds9.reg', 'w') as ds9reg: slits_to_ds9_reg(ds9reg, slits) result = self.create_result( frame=hdulist, slits=slits, positions9=allpos[9], positions7=allpos[7], positions5=allpos[5], positions3=allpos[3], DTU=dtub, ROTANG=rotang, TSUTC1=tsutc1, csupos=csupos, csusens=csusens, ) return result
def run(self, rinput): self.logger.info('starting processing for bars detection') flow = self.init_filters(rinput) hdulist = basic_processing_with_combination(rinput, flow=flow) hdr = hdulist[0].header self.set_base_headers(hdr) self.save_intermediate_img(hdulist, 'reduced_image.fits') try: rotang = hdr['ROTANG'] tsutc1 = hdr['TSUTC1'] dtub, dtur = datamodel.get_dtur_from_header(hdr) csupos = datamodel.get_csup_from_header(hdr) if len(csupos) != 2 * EMIR_NBARS: raise RecipeError('Number of CSUPOS != 2 * NBARS') csusens = datamodel.get_cs_from_header(hdr) except KeyError as error: self.logger.error(error) raise RecipeError(error) self.logger.debug('start finding bars') allpos, slits = find_bars(hdulist, rinput.bars_nominal_positions, csupos, dtur, average_box_row_size=rinput.average_box_row_size, average_box_col_size=rinput.average_box_col_size, fit_peak_npoints=rinput.fit_peak_npoints, median_filter_size=rinput.median_filter_size, logger=self.logger ) self.logger.debug('end finding bars') if self.intermediate_results: with open('ds9.reg', 'w') as ds9reg: slits_to_ds9_reg(ds9reg, slits) result = self.create_result(frame=hdulist, slits=slits, positions9=allpos[9], positions7=allpos[7], positions5=allpos[5], positions3=allpos[3], DTU=dtub, ROTANG=rotang, TSUTC1=tsutc1, csupos=csupos, csusens=csusens, ) return result
def run(self, rinput): self.logger.info('starting processing for bars detection') flow = self.init_filters(rinput) hdulist = basic_processing_with_combination(rinput, flow=flow) hdr = hdulist[0].header self.set_base_headers(hdr) try: rotang = hdr['ROTANG'] tsutc1 = hdr['TSUTC1'] dtub, dtur = datamodel.get_dtur_from_header(hdr) csupos = datamodel.get_csup_from_header(hdr) csusens = datamodel.get_cs_from_header(hdr) except KeyError as error: self.logger.error(error) raise numina.exceptions.RecipeError(error) self.logger.debug('finding bars') # Processed array arr = hdulist[0].data # Median filter of processed array (two times) mfilter_size = rinput.median_filter_size self.logger.debug('median filtering X, %d columns', mfilter_size) arr_median = median_filter(arr, size=(1, mfilter_size)) self.logger.debug('median filtering X, %d rows', mfilter_size) arr_median = median_filter(arr_median, size=(mfilter_size, 1)) # Median filter of processed array (two times) in the other direction # for Y coordinates self.logger.debug('median filtering Y, %d rows', mfilter_size) arr_median_alt = median_filter(arr, size=(mfilter_size, 1)) self.logger.debug('median filtering Y, %d columns', mfilter_size) arr_median_alt = median_filter(arr_median_alt, size=(1, mfilter_size)) xfac = dtur[0] / EMIR_PIXSCALE yfac = -dtur[1] / EMIR_PIXSCALE vec = [yfac, xfac] self.logger.debug('DTU shift is %s', vec) # and the table of approx positions of the slits barstab = rinput.bars_nominal_positions # Currently, we only use fields 0 and 2 # of the nominal positions file # Number or rows used # These other parameters cab be tuned also bstart = 1 bend = 2047 self.logger.debug('ignoring columns outside %d - %d',bstart, bend-1) # extract a region to average wy = (rinput.average_box_row_size // 2) wx = (rinput.average_box_col_size // 2) self.logger.debug('extraction window is %d rows, %d cols',2*wy+1, 2*wx+1) # Fit the peak with these points wfit = 2 * (rinput.fit_peak_npoints // 2) + 1 self.logger.debug('fit with %d points', wfit) # Minimum threshold threshold = 5 * EMIR_RON # Savitsky and Golay (1964) filter to compute the X derivative # scipy >= xx has a savgol_filter function # for compatibility we do it manually allpos = {} ypos3_kernel = None slits = numpy.zeros((EMIR_NBARS, 8), dtype='float') self.logger.info('start finding bars') for ks in [3, 5, 7, 9]: self.logger.debug('kernel size is %d', ks) # S and G kernel for derivative kw = ks * (ks*ks-1) / 12.0 coeffs_are = -numpy.arange((1-ks)//2, (ks-1)//2 + 1) / kw if ks == 3: ypos3_kernel = coeffs_are self.logger.debug('kernel weights are %s', coeffs_are) self.logger.debug('derive image in X direction') arr_deriv = convolve1d(arr_median, coeffs_are, axis=-1) # Axis 0 is # self.logger.debug('derive image in Y direction (with kernel=3)') arr_deriv_alt = convolve1d(arr_median_alt, ypos3_kernel, axis=0) positions = [] for coords in barstab: lbarid = int(coords[0]) rbarid = lbarid + EMIR_NBARS ref_y_coor = coords[1] + vec[1] poly_coeffs = coords[2:] prow = coor_to_pix_1d(ref_y_coor) - 1 fits_row = prow + 1 # FITS pixel index # A function that returns the center of the bar # given its X position def center_of_bar(x): # Pixel values are 0-based return polyval(x+1-vec[0], poly_coeffs) + vec[1] - 1 self.logger.debug('looking for bars with ids %d - %d', lbarid, rbarid) self.logger.debug('reference y position is Y %7.2f', ref_y_coor) # if ref_y_coor is outlimits, skip this bar # ref_y_coor is in FITS format if (ref_y_coor >= 2047) or (ref_y_coor <= 1): self.logger.debug('reference y position is outlimits, skipping') positions.append([lbarid, fits_row, fits_row, 1, 0, 3]) positions.append([rbarid, fits_row, fits_row, 1, 0, 3]) continue # Left bar self.logger.debug('measure left border (%d)', lbarid) centery, xpos, fwhm, st = char_bar_peak_l(arr_deriv, prow, bstart, bend, threshold, center_of_bar, wx=wx, wy=wy, wfit=wfit) xpos1 = xpos positions.append([lbarid, centery+1, fits_row, xpos+1, fwhm, st]) # Right bar self.logger.debug('measure rigth border (%d)', rbarid) centery, xpos, fwhm, st = char_bar_peak_r(arr_deriv, prow, bstart, bend, threshold, center_of_bar, wx=wx, wy=wy, wfit=wfit) positions.append([rbarid, centery+1, fits_row, xpos+1, fwhm, st]) xpos2 = xpos # if st == 0: self.logger.debug('measure top-bottom borders') try: y1, y2, statusy = char_bar_height(arr_deriv_alt, xpos1, xpos2, centery, threshold, wh=35, wfit=wfit) except Exception as error: self.logger.warning('Error computing height: %s', error) statusy = 44 if statusy in [0, 40]: # Main border is detected positions[-1][1] = y2 + 1 positions[-2][1] = y2 + 1 else: # Update status positions[-1][-1] = 4 positions[-2][-1] = 4 else: self.logger.debug('slit is not complete') y1, y2 = 0, 0 # Update positions self.logger.debug('bar %d centroid-y %9.4f, row %d x-pos %9.4f, FWHM %6.3f, status %d', *positions[-2]) self.logger.debug('bar %d centroid-y %9.4f, row %d x-pos %9.4f, FWHM %6.3f, status %d', *positions[-1]) if ks == 5: slits[lbarid - 1] = [xpos1, y2, xpos2, y2, xpos2, y1, xpos1, y1] # FITS coordinates slits[lbarid - 1] += 1.0 self.logger.debug('inserting bars %d-%d into "slits"', lbarid, rbarid) allpos[ks] = numpy.asarray(positions, dtype='float') # GCS doesn't like lists of lists self.logger.debug('end finding bars') result = self.create_result(frame=hdulist, slits=slits, positions9=allpos[9], positions7=allpos[7], positions5=allpos[5], positions3=allpos[3], DTU=dtub, ROTANG=rotang, TSUTC1=tsutc1, csupos=csupos, csusens=csusens, ) return result
def run(self, rinput): logger = logging.getLogger('numina.recipes.emir') logger.info('starting processing for bars detection') flow = self.init_filters(rinput) hdulist = basic_processing_with_combination(rinput, flow=flow) hdr = hdulist[0].header self.set_base_headers(hdr) try: rotang = hdr['ROTANG'] dtub, dtur = datamodel.get_dtur_from_header(hdr) csupos = datamodel.get_csup_from_header(hdr) csusens = datamodel.get_cs_from_header(hdr) except KeyError as error: logger.error(error) raise numina.exceptions.RecipeError(error) logger.debug('finding bars') arr = hdulist[0].data # Median filter logger.debug('median filtering') mfilter_size = rinput.median_filter_size arr_median = median_filter(arr, size=mfilter_size) # Image is mapped between 0 and 1 # for the full range [0: 2**16] logger.debug('image scaling to 0-1') arr_grey = normalize_raw(arr_median) # Find borders logger.debug('find borders') canny_sigma = rinput.canny_sigma # These threshols corespond roughly with # value x (2**16 - 1) high_threshold = rinput.canny_high_threshold low_threshold = rinput.canny_low_threshold edges = canny(arr_grey, sigma=canny_sigma, high_threshold=high_threshold, low_threshold=low_threshold) # Number or rows used # These other parameters cab be tuned also total = 5 maxdist = 1.0 bstart = 100 bend = 1900 positions = [] nt = total // 2 xfac = dtur[0] / EMIR_PIXSCALE yfac = -dtur[1] / EMIR_PIXSCALE vec = [yfac, xfac] logger.debug('DTU shift is %s', vec) # Based on the 'edges image' # and the table of approx positions of the slits barstab = rinput.bars_nominal_positions # Currently, we only use fields 0 and 2 # of the nominal positions file for coords in barstab: lbarid = int(coords[0]) rbarid = lbarid + 55 ref_y_coor = coords[2] + vec[1] prow = coor_to_pix_1d(ref_y_coor) - 1 fits_row = prow + 1 # FITS pixel index logger.debug('looking for bars with ids %d - %d', lbarid, rbarid) logger.debug('reference y position is Y %7.2f', ref_y_coor) # Find the position of each bar bpos = find_position(edges, prow, bstart, bend, total) nbars_found = len(bpos) # If no bar is found, append and empty token if nbars_found == 0: logger.debug('bars %d, %d not found at row %d', lbarid, rbarid, fits_row) thisres1 = (lbarid, fits_row, 0, 0, 1) thisres2 = (rbarid, fits_row, 0, 0, 1) elif nbars_found == 2: # Order values by increasing X centl, centr = sorted(bpos, key=lambda cen: cen[0]) c1 = centl[0] c2 = centr[0] logger.debug('bars found at row %d between %7.2f - %7.2f', fits_row, c1, c2) # Compute FWHM of the collapsed profile cslit = arr_grey[prow - nt:prow + nt + 1, :] pslit = cslit.mean(axis=0) # Add 1 to return FITS coordinates epos, epos_f, error = locate_bar_l(pslit, c1) thisres1 = lbarid, fits_row, epos + 1, epos_f + 1, error epos, epos_f, error = locate_bar_r(pslit, c2) thisres2 = rbarid, fits_row, epos + 1, epos_f + 1, error elif nbars_found == 1: logger.warning( 'only 1 edge found at row %d, not yet implemented', fits_row) thisres1 = (lbarid, fits_row, 0, 0, 1) thisres2 = (rbarid, fits_row, 0, 0, 1) else: logger.warning( '3 or more edges found at row %d, not yet implemented', fits_row) thisres1 = (lbarid, fits_row, 0, 0, 1) thisres2 = (rbarid, fits_row, 0, 0, 1) positions.append(thisres1) positions.append(thisres2) logger.debug('end finding bars') result = self.create_result( frame=hdulist, positions=positions, DTU=dtub, ROTANG=rotang, csupos=csupos, csusens=csusens, param_median_filter_size=rinput.median_filter_size, param_canny_high_threshold=rinput.canny_high_threshold, param_canny_low_threshold=rinput.canny_low_threshold) return result
def run(self, rinput): logger = logging.getLogger('numina.recipes.emir') logger.info('starting processing for bars detection') flow = self.init_filters(rinput) hdulist = basic_processing_with_combination(rinput, flow=flow) hdr = hdulist[0].header self.set_base_headers(hdr) try: rotang = hdr['ROTANG'] dtub, dtur = datamodel.get_dtur_from_header(hdr) csupos = datamodel.get_csup_from_header(hdr) csusens = datamodel.get_cs_from_header(hdr) except KeyError as error: logger.error(error) raise numina.exceptions.RecipeError(error) logger.debug('finding bars') arr = hdulist[0].data # Median filter logger.debug('median filtering') mfilter_size = rinput.median_filter_size arr_median = median_filter(arr, size=mfilter_size) # Image is mapped between 0 and 1 # for the full range [0: 2**16] logger.debug('image scaling to 0-1') arr_grey = normalize_raw(arr_median) # Find borders logger.debug('find borders') canny_sigma = rinput.canny_sigma # These threshols corespond roughly with # value x (2**16 - 1) high_threshold = rinput.canny_high_threshold low_threshold = rinput.canny_low_threshold edges = canny(arr_grey, sigma=canny_sigma, high_threshold=high_threshold, low_threshold=low_threshold) # Number or rows used # These other parameters cab be tuned also total = 5 maxdist = 1.0 bstart = 100 bend = 1900 positions = [] nt = total // 2 xfac = dtur[0] / EMIR_PIXSCALE yfac = -dtur[1] / EMIR_PIXSCALE vec = [yfac, xfac] logger.debug('DTU shift is %s', vec) # Based on the 'edges image' # and the table of approx positions of the slits barstab = rinput.bars_nominal_positions # Currently, we only use fields 0 and 2 # of the nominal positions file for coords in barstab: lbarid = int(coords[0]) rbarid = lbarid + 55 ref_y_coor = coords[2] + vec[1] prow = coor_to_pix_1d(ref_y_coor) - 1 fits_row = prow + 1 # FITS pixel index logger.debug('looking for bars with ids %d - %d', lbarid, rbarid) logger.debug('reference y position is Y %7.2f', ref_y_coor) # Find the position of each bar bpos = find_position(edges, prow, bstart, bend, total) nbars_found = len(bpos) # If no bar is found, append and empty token if nbars_found == 0: logger.debug('bars %d, %d not found at row %d', lbarid, rbarid, fits_row) thisres1 = (lbarid, fits_row, 0, 0, 1) thisres2 = (rbarid, fits_row, 0, 0, 1) elif nbars_found == 2: # Order values by increasing X centl, centr = sorted(bpos, key=lambda cen: cen[0]) c1 = centl[0] c2 = centr[0] logger.debug('bars found at row %d between %7.2f - %7.2f', fits_row, c1, c2) # Compute FWHM of the collapsed profile cslit = arr_grey[prow-nt:prow+nt+1,:] pslit = cslit.mean(axis=0) # Add 1 to return FITS coordinates epos, epos_f, error = locate_bar_l(pslit, c1) thisres1 = lbarid, fits_row, epos + 1, epos_f + 1, error epos, epos_f, error = locate_bar_r(pslit, c2) thisres2 = rbarid, fits_row, epos + 1, epos_f + 1, error elif nbars_found == 1: logger.warning('only 1 edge found at row %d, not yet implemented', fits_row) thisres1 = (lbarid, fits_row, 0, 0, 1) thisres2 = (rbarid, fits_row, 0, 0, 1) else: logger.warning('3 or more edges found at row %d, not yet implemented', fits_row) thisres1 = (lbarid, fits_row, 0, 0, 1) thisres2 = (rbarid, fits_row, 0, 0, 1) positions.append(thisres1) positions.append(thisres2) logger.debug('end finding bars') result = self.create_result(frame=hdulist, positions=positions, DTU=dtub, ROTANG=rotang, csupos=csupos, csusens=csusens, param_median_filter_size=rinput.median_filter_size, param_canny_high_threshold=rinput.canny_high_threshold, param_canny_low_threshold=rinput.canny_low_threshold ) return result
def run(self, rinput): self.logger.info('starting processing for bars detection') flow = self.init_filters(rinput) hdulist = basic_processing_with_combination(rinput, flow=flow) hdr = hdulist[0].header self.set_base_headers(hdr) try: rotang = hdr['ROTANG'] tsutc1 = hdr['TSUTC1'] dtub, dtur = datamodel.get_dtur_from_header(hdr) csupos = datamodel.get_csup_from_header(hdr) csusens = datamodel.get_cs_from_header(hdr) except KeyError as error: self.logger.error(error) raise numina.exceptions.RecipeError(error) self.logger.debug('finding bars') # Processed array arr = hdulist[0].data # Median filter of processed array (two times) mfilter_size = rinput.median_filter_size self.logger.debug('median filtering X, %d columns', mfilter_size) arr_median = median_filter(arr, size=(1, mfilter_size)) self.logger.debug('median filtering X, %d rows', mfilter_size) arr_median = median_filter(arr_median, size=(mfilter_size, 1)) # Median filter of processed array (two times) in the other direction # for Y coordinates self.logger.debug('median filtering Y, %d rows', mfilter_size) arr_median_alt = median_filter(arr, size=(mfilter_size, 1)) self.logger.debug('median filtering Y, %d columns', mfilter_size) arr_median_alt = median_filter(arr_median_alt, size=(1, mfilter_size)) xfac = dtur[0] / EMIR_PIXSCALE yfac = -dtur[1] / EMIR_PIXSCALE vec = [yfac, xfac] self.logger.debug('DTU shift is %s', vec) # and the table of approx positions of the slits barstab = rinput.bars_nominal_positions # Currently, we only use fields 0 and 2 # of the nominal positions file # Number or rows used # These other parameters cab be tuned also bstart = 1 bend = 2047 self.logger.debug('ignoring columns outside %d - %d', bstart, bend - 1) # extract a region to average wy = (rinput.average_box_row_size // 2) wx = (rinput.average_box_col_size // 2) self.logger.debug('extraction window is %d rows, %d cols', 2 * wy + 1, 2 * wx + 1) # Fit the peak with these points wfit = 2 * (rinput.fit_peak_npoints // 2) + 1 self.logger.debug('fit with %d points', wfit) # Minimum threshold threshold = 5 * EMIR_RON # Savitsky and Golay (1964) filter to compute the X derivative # scipy >= xx has a savgol_filter function # for compatibility we do it manually allpos = {} ypos3_kernel = None slits = numpy.zeros((EMIR_NBARS, 8), dtype='float') self.logger.info('start finding bars') for ks in [3, 5, 7, 9]: self.logger.debug('kernel size is %d', ks) # S and G kernel for derivative kw = ks * (ks * ks - 1) / 12.0 coeffs_are = -numpy.arange((1 - ks) // 2, (ks - 1) // 2 + 1) / kw if ks == 3: ypos3_kernel = coeffs_are self.logger.debug('kernel weights are %s', coeffs_are) self.logger.debug('derive image in X direction') arr_deriv = convolve1d(arr_median, coeffs_are, axis=-1) # Axis 0 is # self.logger.debug('derive image in Y direction (with kernel=3)') arr_deriv_alt = convolve1d(arr_median_alt, ypos3_kernel, axis=0) positions = [] for coords in barstab: lbarid = int(coords[0]) rbarid = lbarid + EMIR_NBARS ref_y_coor = coords[1] + vec[1] poly_coeffs = coords[2:] prow = coor_to_pix_1d(ref_y_coor) - 1 fits_row = prow + 1 # FITS pixel index # A function that returns the center of the bar # given its X position def center_of_bar(x): # Pixel values are 0-based return polyval(x + 1 - vec[0], poly_coeffs) + vec[1] - 1 self.logger.debug('looking for bars with ids %d - %d', lbarid, rbarid) self.logger.debug('reference y position is Y %7.2f', ref_y_coor) # if ref_y_coor is outlimits, skip this bar # ref_y_coor is in FITS format if (ref_y_coor >= 2047) or (ref_y_coor <= 1): self.logger.debug( 'reference y position is outlimits, skipping') positions.append([lbarid, fits_row, fits_row, 1, 0, 3]) positions.append([rbarid, fits_row, fits_row, 1, 0, 3]) continue # Left bar self.logger.debug('measure left border (%d)', lbarid) centery, xpos, fwhm, st = char_bar_peak_l(arr_deriv, prow, bstart, bend, threshold, center_of_bar, wx=wx, wy=wy, wfit=wfit) xpos1 = xpos positions.append( [lbarid, centery + 1, fits_row, xpos + 1, fwhm, st]) # Right bar self.logger.debug('measure rigth border (%d)', rbarid) centery, xpos, fwhm, st = char_bar_peak_r(arr_deriv, prow, bstart, bend, threshold, center_of_bar, wx=wx, wy=wy, wfit=wfit) positions.append( [rbarid, centery + 1, fits_row, xpos + 1, fwhm, st]) xpos2 = xpos # if st == 0: self.logger.debug('measure top-bottom borders') try: y1, y2, statusy = char_bar_height(arr_deriv_alt, xpos1, xpos2, centery, threshold, wh=35, wfit=wfit) except Exception as error: self.logger.warning('Error computing height: %s', error) statusy = 44 if statusy in [0, 40]: # Main border is detected positions[-1][1] = y2 + 1 positions[-2][1] = y2 + 1 else: # Update status positions[-1][-1] = 4 positions[-2][-1] = 4 else: self.logger.debug('slit is not complete') y1, y2 = 0, 0 # Update positions self.logger.debug( 'bar %d centroid-y %9.4f, row %d x-pos %9.4f, FWHM %6.3f, status %d', *positions[-2]) self.logger.debug( 'bar %d centroid-y %9.4f, row %d x-pos %9.4f, FWHM %6.3f, status %d', *positions[-1]) if ks == 5: slits[lbarid - 1] = [xpos1, y2, xpos2, y2, xpos2, y1, xpos1, y1] # FITS coordinates slits[lbarid - 1] += 1.0 self.logger.debug('inserting bars %d-%d into "slits"', lbarid, rbarid) allpos[ks] = numpy.asarray( positions, dtype='float') # GCS doesn't like lists of lists self.logger.debug('end finding bars') result = self.create_result( frame=hdulist, slits=slits, positions9=allpos[9], positions7=allpos[7], positions5=allpos[5], positions3=allpos[3], DTU=dtub, ROTANG=rotang, TSUTC1=tsutc1, csupos=csupos, csusens=csusens, ) return result