RR x10
?Do the micrographs need to be unzipped (1 = yes, 0 = no)?
RR x11
?File format (0 = SPIDER, 1 = tif, 2 = PerkinElmer, 3 = ZI)?

x12 = 0  ; these values are left blank for Spider & ZI formats
x13 = 0  ;

IF (x11.EQ.0) GOTO LB3
IF (x11.EQ.3) GOTO LB3
RR x12
?X dimension (width) in pixels?
RR x13
?Y dimension (height) in pixels?

LB3

; for ZI files, pixelsize refers to overview sampling, not original sampling
RR x14
?pixel size (in Angstroms)?
RR x15
?Electron energy (keV)?

RR x31
?window size (pixels)?
RR x32
?actual size (pixels)?
RR x50
?Magnification?
RR x51
?scanning resolution (7,14,etc)?
RR x52
?decimation factor?

; the following values may be converted to interactive mode
;
;?Spherical aberration constant (mm)?
x16 = 2.00
;?Source size (1/A)?
x17 = 0.000
;?Defocus spread (A)?
x18 = 0.000
;?Astigmatism (A)?
x19 = 0.000
;?Azimuth (degrees)?
x20 = 0.000
;?Amplitude contrast ratio (0..1)?
x21 = 0.1
;?Gaussian envelope halfwidth (1/A)?
x22 = 10000.00

FR L
<1>params

; if the file already exists, delete it
IQ FI x88
<1>
IF (x88.EQ.1) THEN
    DE
    <1>
ENDIF

sd / key:      Parameters for single particle reconstruction
<1>
sd /1) zip flag (0 = do not unzip, 1 = needs to be unzipped)
<1>
sd 1,x10
<1>

sd /2) file format (0:SPIDER, 1:HiScan tif, 2:PerkinElmer, 3:ZI Scanner)
<1>
sd 2,x11
<1>

sd /3) micrograph width, in pixels (ignored if this info is in the header)
<1>
sd 3,x12
<1>

sd /4) micrograph height, in pixels (ignored if this info is in the header)
<1>
sd 4,x13
<1>

sd /5) pixel size, in Angstroms
<1>
sd 5,x14
<1>

sd /6) electron energy, in KeV
<1>
sd 6,x15
<1>

sd /7) spherical aberration, mm
<1>
sd 7,x16
<1>

sd /8) source size, 1/A
<1>
sd 8,x17
<1>

sd /9) defocus spread, A
<1>
sd 9,x18
<1>

sd /10) astigmatism, A
<1>
sd 10,x19
<1>

sd /11) azimuth of astigmatism, degrees
<1>
sd 11,x20
<1>

sd /12) amplitude contrast ratio
<1>
sd 12,x21
<1>

sd /13) Gaussian envelope halfwidth, 1/A
<1>
sd 13,x22
<1>

; compute lambda from kv
x30 = 12.398 / SQR(x15 * (1022.0 + x15))
sd /14) Lambda, A
<1>
sd 14,x30
<1>

; compute max.spat.freq. from pixel size
x30 = 1.0 / (2.0 * x14)
sd /15) maximum spatial frequency, 1/A
<1>
sd 15,x30
<1>

sd /16) decimation factor
<1>
sd 16,x52
<1>

sd /17) particle window size, pixels 
<1>
sd 17,x31
<1>

sd /18) actual size of particle, pixels
<1>
sd 18,x32
<1>

sd /19) magnification
<1>
sd 19,x50
<1>

sd /20) scanning resolution (7 or 14 microns)
<1>
sd 20,x51
<1>


VM
echo Parameters saved to <1>.$DATEXT

EN D