; Creates parameter file for reconstruction
;
; SOURCE: spider/docs/techs/recon/newprogs/makeparams.spi
;
; PURPOSE: Creates parameter file, including values for
; lambda, spatial frequency, window size, particle size
; ----------- Registers ------------------------
; Default values for ribosomes (only used if zero is input for query below)
[ws] = 368 ; Angstroms, default typical window size for ribosome projects
[diam] = 250 ; Angstroms, default actual ribosome particle diameter
; Following values may be converted to interactive mode
;?Spherical aberration constant (mm)?
[sp_sph_abb] = 2.00
;?Source size (1/A)?
[sp_sourcesiz] = 0.000
;?Defocus spread (A)?
[sp_def_spr] = 0.000
;?Astigmatism (A)?
[sp_astig] = 0.000
;?Azimuth (degrees)?
[sp_az_astig] = 0.000
;?Amplitude contrast ratio (0..1)?
[sp_acr] = 0.1
;?Gaussian envelope halfwidth (1/A)?
[sp_geh] = 10000.00
; ----------- Input files ----------------------
; ----------- Output files ---------------------
[docfile] = 'params'
[lisfile] = 'params_lis'
; -------------- END BATCH HEADER --------------------------
; -------------- Interactive input --------------------------
RR [sp_zipflag]
?Do the micrographs need to be unzipped (1 = yes, 0 = no)?
RR [sp_format]
?File format (0 = SPIDER, 1 = TIF, 2 = PerkinElmer, 3 = ZI, 4 = Nikon)?
[sp_xm] = 0 ; These values are left blank for SPIDER & ZI formats
[sp_ym] = 0 ;
IF ([sp_format].NE.0) THEN
IF ([sp_format].ne.3) THEN
RR [sp_xm]
?X dimension (width) in pixels?
RR [sp_ym]
?Y dimension (height) in pixels?
ENDIF
ENDIF
; For ZI files, pixelsize refers to overview sampling, not original sampling
RR [sp_pixsiz]
?Pixel size (in Angstroms)?
RR [sp_kev]
?Electron energy (keV)?
RR [sp_winsiz]
?Window size (pixels)?
IF ([sp_winsiz].EQ.0) THEN ; Use default window size
[sp_winsiz] = INT([ws]/[sp_pixsiz]) ; Compute window size (pixels)
; Ensure window size is odd
[xwt] = INT([sp_winsiz]/2.0)
[v90] = [sp_winsiz] - (2*[xwt])
if ([v90].EQ.0) [sp_winsiz] = [sp_winsiz] + 1
ENDIF
RR [sp_partsiz]
?Actual size (pixels)?
IF ([sp_partsiz].EQ.0) THEN ; Use default particle size
[sp_partsiz] = INT([diam]/[sp_pixsiz]) ; Compute particle size (pixels)
ENDIF
RR [sp_mag]
?Magnification?
RR [sp_scanres]
?Scanning resolution (7, 14, etc)?
RR [sp_dec]
?Decimation factor?
; -------------- Compute dependent parameters ---------------------------------
; Compute lambda from kev
[sp_lambda] = 12.398 / SQR([sp_kev] * (1022.0 + [sp_kev]))
; Compute max. spatial freq. from pixel size
[sp_maxspfreq] = 1.0 / (2.0 * [sp_pixsiz])
; -------------- Output parameters to procedure file --------------------------
; Delete existing output files
DE
[lisfile]
VM
echo '; Parameters for single particle reconstruction' >> [lisfile].$DATEXT
VM
echo -n '; $PRJEXT/$DATEXT ' >> [lisfile].$DATEXT
VM
date >> [lisfile].$DATEXT
VM
echo ' ' >> [lisfile].$DATEXT
VM
echo [sp_zipflag] = ' ' {%f8.3%[sp_zipflag]} \; Zip flag \(0: Do not unzip, 1: Must unzip\) >> [lisfile].$DATEXT
VM
echo [sp_format] = ' ' {%f8.3%[sp_format]} \; File format \(0:SPIDER, 1:HiScan TIF, 2:PE, 3:ZI \) >> [lisfile].$DATEXT
VM
echo [sp_xm] = ' ' {%f8.3%[sp_xm]} \; Micrograph width, pixels \(ignored if present in header\) >> [lisfile].$DATEXT
VM
echo [sp_ym] = ' ' {%f8.3%[sp_ym]} \; Micrograph height, pixels \(ignored if present in header\) >> [lisfile].$DATEXT
VM
echo [sp_pixsiz] = ' ' {%f8.3%[sp_pixsiz]} \; Pixel size, A >> [lisfile].$DATEXT
VM
echo [sp_kev] = ' ' {%f8.3%[sp_kev]} \; Electron energy, KeV >> [lisfile].$DATEXT
VM
echo [sp_sph_abb] = ' ' {%f8.3%[sp_sph_abb]} \; Spherical aberration, mm >> [lisfile].$DATEXT
VM
echo [sp_sourcesiz] = ' ' {%f8.3%[sp_sourcesiz]} \; Source size, 1/A >> [lisfile].$DATEXT
VM
echo [sp_def_spr] = ' ' {%f8.3%[sp_def_spr]} \; Defocus spread, A >> [lisfile].$DATEXT
VM
echo [sp_astig] = ' ' {%f8.3%[sp_astig]} \; Astigmatism, A >> [lisfile].$DATEXT
VM
echo [sp_az_astig] = ' ' {%f8.3%[sp_az_astig]} \; Azimuth of astigmatism, degrees >> [lisfile].$DATEXT
VM
echo [sp_acr] = ' ' {%f8.3%[sp_acr]} \; Amplitude contrast ratio >> [lisfile].$DATEXT
VM
echo [sp_geh] = ' ' {%f11.4%[sp_geh]} \; Gaussian envelope halfwidth, 1/A >> [lisfile].$DATEXT
VM
echo [sp_lambda] = ' ' {%f8.3%[sp_lambda]} \; Lambda >> [lisfile].$DATEXT
VM
echo [sp_maxspfreq] = ' ' {%f8.3%[sp_maxspfreq]} \; Maximum spatial frequency, 1/A >> [lisfile].$DATEXT
VM
echo [sp_dec] = ' ' {%f8.3%[sp_dec]} \; Decimation factor >> [lisfile].$DATEXT
VM
echo [sp_winsiz] = ' ' {%f8.3%[sp_winsiz]} \; Particle window size, pixels >> [lisfile].$DATEXT
VM
echo [sp_partsiz] = ' ' {%f8.3%[sp_partsiz]} \; Size of particle, pixels >> [lisfile].$DATEXT
VM
echo [sp_mag] = ' ' {%f8.3%[sp_mag]} \; Magnification >> [lisfile].$DATEXT
VM
echo [sp_scanres] = ' ' {%f8.3%[sp_scanres]} \; Scanning resolution \(7 or 14 microns\) >> [lisfile].$DATEXT
VM
echo ' RE' >> [lisfile].$DATEXT
VM
echo ' 'Reconstruction Parameters saved to [lisfile].$DATEXT
; -------------- Output parameters to doc file --------------------------
; Delete existing output files
DE
[docfile]
SD / key: Parameters for single particle reconstruction
[docfile]
SD /1) Zip flag (0 = Do not unzip, 1 = Needs to be unzipped)
[docfile]
SD 1,[sp_zipflag]
[docfile]
SD /2) File format (0:SPIDER, 1:HiScan tif, 2:PerkinElmer, 3:ZI Scanner)
[docfile]
SD 2,[sp_format]
[docfile]
SD /3) Micrograph width, in pixels (ignored if present in header)
[docfile]
SD 3,[xm]
[docfile]
SD /4) Micrograph height, pixels (ignored if present in header)
[docfile]
SD 4,[sp_ym]
[docfile]
SD /5) Pixel size, A
[docfile]
SD 5,[sp_pixsiz]
[docfile]
SD /6) Electron energy, KeV
[docfile]
SD 6,[sp_kev]
[docfile]
SD /7) Spherical aberration, mm
[docfile]
SD 7,[sp_sph_abb]
[docfile]
SD /8) Source size, 1/A
[docfile]
SD 8,[sp_sourcesiz]
[docfile]
SD /9) Defocus spread, A
[docfile]
SD 9,[sp_def_spr]
[docfile]
SD /10) Astigmatism, A
[docfile]
SD 10,[sp_astig]
[docfile]
SD /11) Azimuth of astigmatism, degrees
[docfile]
SD 11,[sp_az_astig]
[docfile]
SD /12) Amplitude contrast ratio
[docfile]
SD 12,[sp_acr]
[docfile]
SD /13) Gaussian envelope halfwidth, 1/A
[docfile]
SD 13,[sp_geh]
[docfile]
SD /14) Lambda, A
[docfile]
SD 14,[sp_lambda]
[docfile]
SD /15) Maximum spatial frequency, 1/A
[docfile]
SD 15,[sp_maxspfreq]
[docfile]
SD /16) Decimation factor
[docfile]
SD 16,[sp_dec]
[docfile]
SD /17) Particle window size, pixels
[docfile]
SD 17,[sp_winsiz]
[docfile]
SD /18) Actual size of particle, pixels
[docfile]
SD 18,[sp_partsiz]
[docfile]
SD /19) Magnification
[docfile]
SD 19,[sp_mag]
[docfile]
SD /20) Scanning resolution (7 or 14 microns)
[docfile]
SD 20,[sp_scanres]
[docfile]
SD E
[docfile]
VM
echo ' 'Reconstruction Parameters saved to [docfile].$DATEXT
VM
echo ' '
RE