; Creates parameter file for reconstruction
;
; SOURCE: spider/docs/techs/recon1/Procs/make-params.spi
;
; PURPOSE: Creates parameter file, including values for
; lambda, spatial frequency, window size, particle size, etc.
;
; USAGE: clean ; ./spider spi/dat @make-params
; ----------- Registers ------------------------
; Following values may be converted to interactive mode
; Default values for ribosomes (only used if zero is input for query below)
[diam] = 276 ; Angstroms, default actual ribosome particle diameter
;? Source size, 1/A )?
[sp_sourcesiz] = 0.000 ; Usually OK. This value = no effect on phase flipping CTF
;? Defocus spread, A )?
[sp_def_spread] = 0.000 ; Usually OK. This value = no effect on phase flipping CTF
;? Astigmatism, A ?
[sp_astig] = 0.000 ; None. Usually OK if microscope is well adjusted
;? Azimuth, degrees ?
[sp_az_astig] = 0.000 ; None. Usually OK if microscope is well adjusted
;? Amplitude contrast ratio (0..1) ?
[sp_acr] = 0.1 ; Used for CTF correction. Usual value
;? Gaussian envelope halfwidth ?
[sp_geh] = 10000.00 ; Used for CTF correction, This value = no effect on phase flipping CTF
; ----------- Input files ----------------------
; ----------- Output files ---------------------
[docfile] = 'params'
[lisfile] = 'params-set'
; -------------- 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, 5 = MRC)?
[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
IF ([sp_format].NE.5) THEN
RR [sp_xm]
?X dimension (width) in pixels?
RR [sp_ym]
?Y dimension (height) in pixels?
ENDIF
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_sph_abb]
?Spherical aberration constant (mm)?
RR [sp_partsiz]
?Particle size, pixels (0 for ribosome default)?
IF ([sp_partsiz].EQ.0) THEN ; Use default particle size
[sp_partsiz] = INT([diam]/[sp_pixsiz]) ; Compute particle size (pixels)
SYS
echo "Using particle size of {%i0%[sp_partsiz]} pixels" ; echo
ENDIF
RR [sp_winsiz]
?Window size, pixels (0 for default)?
IF ([sp_winsiz].EQ.0) THEN ; Use default window size
[sp_winsiz] = INT([sp_partsiz]*4/3) ; Compute window size (pixels)
; Ensure window size is even
[xwt] = INT([sp_winsiz]/2.0)
[v90] = [sp_winsiz] - (2*[xwt])
IF ([v90] .NE. 0) [sp_winsiz] = [sp_winsiz] + 1
SYS
echo "Using window size of {%i0%[sp_winsiz]} pixels" ; echo
ENDIF
RR [sp_mag]
?Magnification?
RR [sp_scanres] ; Scanning resolution = DetectorPixelSize, um (Usually: 7 or 14)
? Detector pixel size, um (7, 14, ...)?
RR [sp_dec]
? Decimation factor ?
; -------------- Compute dependent parameters ---------------------------------
; Compute relativistic lambda from kev
[sp_lambda] = 12.398 / SQR([sp_kev] * (1022.0 + [sp_kev]))
; Compute max. spatial freq. from pixel size
[sp_max_spfreq] = 1.0 / (2.0 * [sp_pixsiz])
; -------------- Output parameters to procedure file --------------------------
; Delete existing output files
DE
[lisfile]
SYS
echo ' ; Parameters for single particle reconstruction' >> [lisfile].$DATEXT
SYS
echo -n ' ; $PRJEXT/$DATEXT ' >> [lisfile].$DATEXT
SYS
date >> [lisfile].$DATEXT
SYS
echo ' ' >> [lisfile].$DATEXT
SYS
echo ' [sp_zipflag] = ' {%f8.0%[sp_zipflag]} \; Zip flag \(0: Do not unzip, 1: Must unzip\) >> [lisfile].$DATEXT
SYS
echo ' [sp_format] = ' {%f8.0%[sp_format]} \; File format \(0:SPIDER, 1:HiScan TIF, 2:PE, 3:ZI \) >> [lisfile].$DATEXT
SYS
echo ' [sp_xm] = ' {%f8.0%[sp_xm]} \; Micrograph width, pixels \(ignored if present in header\) >> [lisfile].$DATEXT
SYS
echo ' [sp_ym] = ' {%f8.0%[sp_ym]} \; Micrograph height, pixels \(ignored if present in header\) >> [lisfile].$DATEXT
SYS
echo ' [sp_pixsiz] = ' {%f8.2%[sp_pixsiz]} \; Pixel size, A >> [lisfile].$DATEXT
SYS
echo ' [sp_kev] = ' {%f8.2%[sp_kev]} \; Electron energy, KeV >> [lisfile].$DATEXT
SYS
echo ' [sp_sph_abb] = ' {%f8.3%[sp_sph_abb]} \; Spherical aberration, mm >> [lisfile].$DATEXT
SYS
echo ' [sp_sourcesiz] = ' {%f8.3%[sp_sourcesiz]} \; Source size, 1/A >> [lisfile].$DATEXT
SYS
echo ' [sp_def_spread] = ' {%f8.3%[sp_def_spread]} \; Defocus spread, A >> [lisfile].$DATEXT
SYS
echo ' [sp_astig] = ' {%f8.1%[sp_astig]} \; Astigmatism, A >> [lisfile].$DATEXT
SYS
echo ' [sp_az_astig] = ' {%f8.2%[sp_az_astig]} \; Azimuth of astigmatism, degrees >> [lisfile].$DATEXT
SYS
echo ' [sp_acr] = ' {%f8.3%[sp_acr]} \; Amplitude contrast ratio >> [lisfile].$DATEXT
SYS
echo ' [sp_geh] = ' {%f9.2%[sp_geh]} \; Gaussian envelope halfwidth >> [lisfile].$DATEXT
SYS
echo ' [sp_lambda] = ' {%f8.5%[sp_lambda]} \; Lambda, A >> [lisfile].$DATEXT
SYS
echo ' [sp_max_spfreq] = ' {%f8.3%[sp_max_spfreq]} \; Maximum spatial frequency, 1/A >> [lisfile].$DATEXT
SYS
echo ' [sp_dec] = ' {%f8.1%[sp_dec]} \; Decimation factor >> [lisfile].$DATEXT
SYS
echo ' [sp_winsiz] = ' {%f8.1%[sp_winsiz]} \; Particle window size, pixels >> [lisfile].$DATEXT
SYS
echo ' [sp_partsiz] = ' {%f8.1%[sp_partsiz]} \; Size of particle, pixels >> [lisfile].$DATEXT
SYS
echo ' [sp_mag] = ' {%f10.1%[sp_mag]} \; Magnification >> [lisfile].$DATEXT
SYS
echo ' [sp_scanres] = ' {%f8.1%[sp_scanres]} \; Detector pixel size, um >> [lisfile].$DATEXT
SYS
echo ' ' >> [lisfile].$DATEXT
SYS
echo ' RE' >> [lisfile].$DATEXT
SYS
echo ' 'Reconstruction Parameters saved in: [lisfile].$DATEXT
; -------------- Output parameters to doc file --------------------------
; Delete existing output file
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_spread]
[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
[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_max_spfreq]
[docfile]
SD /16) Decimation factor (Usually unused)
[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) Detector Pixel Size, um (Usually: 7 or 14)
[docfile]
SD 20,[sp_scanres]
[docfile]
SD E
[docfile]
SYS
echo ' 'Reconstruction Parameters saved in: [docfile].$DATEXT
SYS
echo ' '
EN
; --------------------------- Unused below here -------------------------------
; Test data
0
1
0
0
1.1
300
400
368
112000
14
1
; Modified 2016-05-24
; 2016-01-14 (trs) -- added option for MRC format