|
and |
IMPMC, CNRS UMR 7590 Campus Boucicaut, Université Paris 6 140 Rue de Lourmel 75015 Paris |
The batches displayed in this practical session were written for the SPIDER Unix version number 14.16 issued in 2006. These batches should run on your workstation if you possess a more recent Spider version.
;-------------------------------------------------------------------------! ; b00.fed/hbl : batch to read back raw format images and translate them ! ; in a spider format compatible with your own spider version ! ;-------------------------------------------------------------------------! md tr on ; If this batch does not work please check in you manual the ; spider operation "cp from raw". It might have changed with newer ; spider versions. Here it works like this : ; ; cp from raw <--- Name of the operation ; rawmic001 <--- Input image file name ; 8 <--- 8 bytes coding ; 736,780,1 <--- width,length,thickness (NSAM,NROW,NSLICE) ; 0 <--- Number of Header bytes to be skipped ; scr002 <--- Output spider file ; ; ;-----[ translate rawmic001.hbl into mic001.hbl : cp from raw ../micrographs/rawmic001 8 736,780,1 0 scr001 ; Find Fmax=x11 and Fmin=x12 densities fs x11,x12 scr001 ; Compute dynamic range (Fmax-Fmin)=x15 x15=x11-x12 ; rescale image densities between 0.0 and 1.0 ar scr001 ../micrographs/mic001 ((P1-X12)/X15) ;-----[ Reduce mic001.hbl by a factor of 2 into pic001.hbl ip ../micrographs/mic001 ../micrographs/pic001 368,390 ;-----[ translate rawmic002.hbl into mic002.hbl : cp from raw ../micrographs/rawmic002 8 1100,780,1 0 scr002 ; Find Fmax=x11 and Fmin=x12 densities fs x11,x12 scr002 ; Compute dynamic range (Fmax-Fmin)=x15 x15=x11-x12 ; rescale image densities between 0.0 and 1.0 ar scr002 ../micrographs/mic002 ((P1-X12)/X15) ;-----[ Reduce mic002.hbl by a factor of 2 into pic002.hbl ip ../micrographs/mic002 ../micrographs/pic002 550,390 ; Delete intermediate files : de scr001 de scr002 en
; hbl/hbl dcu001.hbl Tue Feb 13 16:49:44 2005 0001 6 1.000000 568.000000 288.000000 284.000000 144.000000 1.000000 0002 6 2.000000 62.000000 44.000000 31.000000 22.000000 1.000000 0003 6 3.000000 96.000000 644.000000 48.000000 322.000000 1.000000 0004 6 4.000000 940.000000 52.000000 470.000000 26.000000 1.000000 0005 6 5.000000 950.000000 428.000000 475.000000 214.000000 1.000000 0006 6 6.000000 896.000000 668.000000 448.000000 334.000000 1.000000 0007 6 7.000000 424.000000 600.000000 212.000000 300.000000 1.000000 0008 6 8.000000 340.000000 312.000000 170.000000 156.000000 1.000000 0009 6 9.000000 288.000000 242.000000 144.000000 121.000000 1.000000 0010 6 10.000000 324.000000 172.000000 162.000000 86.000000 1.000000 0011 6 11.000000 268.000000 106.000000 134.000000 53.000000 1.000000 0012 6 12.000000 204.000000 158.000000 102.000000 79.000000 1.000000 0013 6 13.000000 160.000000 84.000000 80.000000 42.000000 1.000000 0014 6 14.000000 62.000000 122.000000 31.000000 61.000000 1.000000 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1.000000 0067 6 67.000000 436.000000 642.000000 218.000000 321.000000 1.000000 0068 6 68.000000 446.000000 734.000000 223.000000 367.000000 1.000000 0069 6 69.000000 518.000000 646.000000 259.000000 323.000000 1.000000 0070 6 70.000000 576.000000 590.000000 288.000000 295.000000 1.000000 0071 6 71.000000 690.000000 494.000000 345.000000 247.000000 1.000000 0072 6 72.000000 664.000000 566.000000 332.000000 283.000000 1.000000 0073 6 73.000000 688.000000 638.000000 344.000000 319.000000 1.000000 0074 6 74.000000 680.000000 732.000000 340.000000 366.000000 1.000000 0075 6 75.000000 548.000000 722.000000 274.000000 361.000000 1.000000 0076 6 76.000000 612.000000 346.000000 306.000000 173.000000 1.000000 ; hbl/hbl dcb001.hbl Tue Feb 13 17:18:19 2005 0121 6 0.000000 0.000000 0.000000 0.000000 7.000000 0.000000 ; FITTED flag 0122 6 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ; X0,Y0 ORIG. IN 0 DEG IM., XS0,YS0 ORIG. IN TILTED IM. REDUCTION FACTOR 0123 6 284.000000 144.000000 191.033218 143.713867 2.000000 0.000000 ; TILTANGLE, AXIS DIR. IN: 0 DEG IM. THETA GAMMA PHI 0124 6 48.954857 -0.237597 -0.333951 0.000000 0.000000 0.000000
;---------------------------------------------------------------------------!
; b01.fed/hbl : batch for boxing images from the 45 degree tilted specimen :
;---------------------------------------------------------------------------!
; PARAMETERS
x76=76 ; last image number
x81=100. ; image dimension
x82=x81/2. ; 1/2 image dimension
; INPUTS:
fr l
[init_tilted_coords]../doc/dct001 ; tilted image coordinates (from WEB)
fr l
[tilted_micrograph]../micrographs/mic001 ; tilted micrograph
; OUTPUTS:
fr l
[tilted_images]../images/tilt{*****x10} ; windowed, tilted images
fr l
[new_tilted_coords]../doc/dwintilt ; new tilted image coordinates
; END BATCH HEADER
;---------------------------------------------------------------------------!
md
tr on
;-----[ Starts the do loop of the boxing :
do lb1 x10=1,x76
; reads central X and Y coordinates for each particle in the micrograph
ud x10,x11,x12,x13,x14,x15,x16
[init_tilted_coords]
; subtract 1/2 image dimension from center coordinates
X12=X12-x82
X13=X13-x82
; boxing out of each particle in a set of small images
wi
[tilted_micrograph]
[tilted_images]
X81,X81
X12,X13
; save windowing (top left) coordinates in a new document file
sd x10,x12,x13
[new_tilted_coords]
lb1
en
;-----------------------------------------------------------------!
; b02.fed/hbl : batch for boxing images from the untilted specimen:
;-----------------------------------------------------------------!
; PARAMETERS
x76=76 ; last image number
x81=100. ; image dimension
x82=x81/2. ; 1/2 image dimension
; INPUTS:
fr l
[init_untilted_coords]../doc/dcu001 ; untilted image coos (from WEB)
fr l
[untilted_micrograph]../micrographs/mic002 ; untilted micrograph
; OUTPUTS:
fr l
[untilted_images]../images/unt{*****x10} ; windowed, untilted images
fr l
[new_untilted_coords]../doc/dwinunt ; new untilted image coordinates
; END BATCH HEADER
;-----------------------------------------------------------------!
md
tr on
;-----[ Starts the do loop of the boxing :
do lb1 x10=1,x76
; reads central X and Y coordinates for each particle in the micrograph
ud x10,x11,x12,x13,x14,x15,x16
[init_untilted_coords]
; subtract 1/2 image dimension from center coordinates
X12=X12-x82
X13=X13-x82
; boxing out of each particle in a set of small images
wi
[untilted_micrograph]
[untilted_images]
x81,x81
X12,X13
; save windowing (top left) coordinates in a new document file
sd x10,x12,x13
[new_untilted_coords]
lb1
en
;-----------------------------------------------------------------------------!
; b03.fed/hbf : - iterative reference free alignment untilted-specimen images
; - first part using AP SR reference free alignment :
;-----------------------------------------------------------------------------!
; PARAMETERS:
X63=1. ; first image number
X62=76. ; last image number
x50=100 ; image dimension
x51=x50/2+1 ; image center coordinates
; INPUT:
fr l
[untilted_images]../images/unt ; untilted windowed image filename template
; OUTPUTS:
fr l
[masked_untilted]../images/mas ; untilted masked images
fr l
[apsr_image]../r2d/avs*** ; AP SR output images
fr l
[apsr_doc]../doc/davs*** ; AP SR output doc files
; END BATCH HEADER
;-----------------------------------------------------------------------------!
md
tr on
;-----------------------------------------------------------------------------!
; Apply a circular mask with Gaussian edge on all images
;-----------------------------------------------------------------------------!
; loop through particles
DO LB1 x10=X63,X62
; apply a circular mask on the raw images and stack them
ma
[untilted_images]{*****x10}
[masked_untilted]{*****x10}
(47.) ; mask radius
g ; Gaussian cutoff
c ; background set to circumference average
x51,x51 ; mask center
(2.5) ; Gaussian falloff
LB1
;-----------------------------------------------------------------------------!
; Apply a reference free alignment as developped by
; Pawel Penczek et al., Ultramicroscopy 40 (1992) 33-53
;-----------------------------------------------------------------------------!
ap sr
[masked_untilted]*****
x63-x62 ; first and last image numbers
(75) ; expected size of the particle in pixels
(5,38) ; first and last rings used for rotationnal alignment
* ; image to use for centering (* = a gaussian disk is used)
[apsr_image] ; template for output global images
[apsr_doc] ; template for output doc files
;-----------------------------------------------------------------------------!
; Show how many cycles were necessary for reference free alignment
vm
ls -l ../r2d/avs*
vm
ls -l ../doc/davs*
; delete intermediate files
de a
[masked_untilted]00001
en
;-----------------------------------------------------------------------------!
; b04.fed/hbf : - check last cycle of reference free alignment with respect
; - to horizontal and/or vertical orientation
;-----------------------------------------------------------------------------!
md
tr on
; PARAMETERS:
X61=4. ; ending cycle number in the reference free alignment of b03.new
X63=1. ; first image number
X62=76. ; last image number
X71=1. ; starting cycle number
x50=100 ; image dimension
; INPUT:
fr l
[untilted_images]../images/unt ; untilted windowed image filename template
fr l
[masked_untilted]../images/mas ; untilted masked images
fr l
[apsr_image]../r2d/avs*** ; AP SR output images
fr l
[apsr_doc]../doc/davs*** ; AP SR output doc files
; OUTPUTS:
fr l
[solapsr]../r2d/solapsr ; two solutions final images
fr l
[doc_solapsr]../doc/dsolapsr ; doc file with the two solutions
fr l
[MONTAGE]../r2d/MALIGN ; montage of the intermediate images
; END BATCH HEADER
;-----------------------------------------------------------------------------!
; check alignment of the last reference free image with its mirror inversion
;-----------------------------------------------------------------------------!
; get the size of the last apsr_image
fi n x21
[apsr_image]x61
(2)
x80=128
x81=(x80-x21)/2.
; Put the average of cycle 3 in a larger image (128 x 128 pixels)
pd
[apsr_image]x61
scr001
x80,x80
b
x81,x81
; Compute the mirror inverted copy of this image
mr
scr001
scr002
Y
; Compute the autocorrelation of the original image
ac ic
scr001
scr003
; Compute the autocorrelation of the mirror inverted image
ac ic
scr002
scr004
; Angular cross-correlation of the two autocorrelation functions
; (rotation angle is kept in register x10)
or 2,x10,x90
scr004
scr003
(5,60)
(1)
(F)
;-----------------------------------------------------------------------------!
; TWO SOLUTIONS CAN BE FOUND TO GET THE DESIRED ORIENTATION OF YOUR IMAGES :
; Solution No.1 : apply a half rotation angle -x10/2.
; Solution No.2 : apply solution No.1 + 90 degrees
;-----------------------------------------------------------------------------!
x55=1.
; Apply a rotation of -x10/2. => Y axis = cylinder axis )
x11=-x10/2.
rt
[apsr_image]x61
scr005
x11
; Search the new center of gravity of the rotated average
cg ph x21,x22,x12,x13
scr005
x12=-x12
x13=-x13
; rotation and translation of the first solution
rt sq
[apsr_image]x61
[solapsr]{***x55}
x11
x12,x13
; save rotation and X Y shifts for solution No.1
sd x55,x11,X12,X13
[doc_solapsr]
;-----------------------------------------------------------------------------!
; Solution No.2 : apply solution No.1 + 90 degrees
;-----------------------------------------------------------------------------!
x55=2.
x17=x11+90.
rt
[apsr_image]x61
scr006
x17
; Search the new center of gravity of the rotated average
cg ph x21,x22,x12,x13
scr006
x12=-x12
x13=-x13
; rotation and translation of the +90 degree solution
rt sq
[apsr_image]x61
[solapsr]{***x55}
x17
x12,x13
; save rotation and X Y shifts for solution No.2
sd x55,x17,X12,X13
[doc_solapsr]
;-----------------------------------------------------------------------------!
; Creates a montage with intermediate images of
; solution No.1 left column of the montage
; solution No.2 right column of the montage
;-----------------------------------------------------------------------------!
; put solution No.1 into 128x128 pixels format
pd
[solapsr]001
scr005
x80,x80
b
x81,x81
; put solution No.2 into 128x128 pixels format
pd
[solapsr]002
scr006
x80,x80
b
x81,x81
; Create montage file with two columns
mn s
scr***
1-6
2,2
2.
[MONTAGE]
; remove intermediate images
;de a
;scr001
en
;-----------------------------------------------------------------------------!
; b05.fed/hbf : - after reference free alignment and visual checking
; - apply solution No.1 or 2. to all original files
;-----------------------------------------------------------------------------!
md
tr on
; PARAMETERS:
X61=4. ; ending reference free alignment cycle number
X10=2. ; solution choosed No.1 or No.2 for final orientation of particles
x60=x61+1. ; additional and last alignment cycle number
;
X63=1. ; first image number
X62=76. ; last image number
x50=100 ; image dimension
x51=(x50/2.)+1 ; image central coordinates
; INPUT:
fr l
[untilted_images]../images/unt ; untilted windowed image filename template
fr l
[doc_solapsr]../doc/dsolapsr ; doc file with the two solutions
fr l
[apsr_doc]../doc/davs ; AP SR output doc files
; OUTPUTS:
fr l
[aligned_untilt]../images/cenu ; untilted aligned image filename template
fr l
[align_doc_untilt]../doc/dalu ; untilted alignment doc file
fr l
[untilted_avg]../r2d/avgu ; untilted centered average filename template
fr l
[untilted_var]../r2d/varu ; untilted variance template for centered avg
; END BATCH HEADER
;-----------------------------------------------------------------------------!
; get rotation and shift from the designated solution:
ud x10,x11,x12,x13
[doc_solapsr]
; loop through images
do lb5 X90=x63,x62
ud ic X90,X82,X84,X85
[apsr_doc]{***x61}
; apply sum alignment
sa p,X82,X84,X85,X11,X12,X13,X52,X54,X55
; save new rotation and shifts in an additional alignment doc file
sd X90,X52,X54,X55
[align_doc_untilt]001
; rotation & centering of raw untilted images (unt*****.hbl):
rt sq
[untilted_images]{*****X90}
scr004
X52
X54,X55
; Apply a circular mask on the aligned and centered images
ma
scr004
[aligned_untilt]{*****X90}
(46.) ; mask radius
g ; Gaussian cutoff
c ; background set to circumference average
x51,x51 ; mask center
(2.5) ; Gaussian falloff
lb5
ud ice ; close doc file
[apsr_doc]{***x61}
; Computation of the average and variance maps of the last cycle
as dc
[aligned_untilt]*****
x63-x62
A
[untilted_avg]001
[untilted_var]001
; Deletes intermediate files or images
de
scr004
en
;-----------------------------------------------------------------------------!
; b06.fed/hbf : - Centering of the tilted-specimen images
;-----------------------------------------------------------------------------!
md
tr on
; PARAMETERS:
X63=1. ; first image number
X62=76. ; last image number
x50=100 ; image dimension
x51=x50/2+1 ; image center coordinates
; INPUTS:
fr l
[tilted_images]../images/tilt ; tilted windowed image filename template
; OUTPUTS:
fr l
[dummy_rotate]../doc/dummy ; tilted rotation doc filename template
fr l
[aligned_tilted]../images/cent ; tilted aligned tilted image filename template
fr l
[shift_doc_tilt]../doc/dshiftt ; tilted shift doc filename template
fr l
[apsa_avg_tilt]../r2d/avst ; tilted intermediate avg filename template
fr l
[alignment_doc]../doc/dalt ; tilted alignment doc filename template
fr l
[tilted_avg]../r2d/avgt ; tilted centered average filename template
fr l
[tilted_var]../r2d/vart ; tilted variance template for centered avg
;-----------------------------------------------------------------------------!
; Create a dummy doc file corresponding to a rotational alignment
; where a zero degree rotation angle would be found for all images
; dummy variables for initial doc file
X31=0.0
x32=1.
DO LB1 X10=x63,x62
SD X0,X0,X31,X32,X32
[dummy_rotate]
; Apply a circular mask on all the images
ma
[tilted_images]{*****X10}
[aligned_tilted]{*****X10}
(47.) ; mask radius
g ; Gaussian cutoff
c ; background set to circumference average
x51,x51 ; mask center
(2.5) ; Gaussian falloff
LB1
; Alignment by translation on all the masked images
AP SA
[aligned_tilted]00001
[dummy_rotate]
(1) ; group number from AP RA (set to dummy variable x32=1)
N ; not checking 360-degree range
[shift_doc_tilt]001
[apsa_avg_tilt]001
; Search the center of gravity of the global average map AVSTX71
cg ph X21,X22
[apsa_avg_tilt]001
; Apply X&Y translation (minus location of center of gravity)
; to all raw tilted-specimen images
DO LB4 X30=1,76
UD IC X30,X31,X32,X33,X34,X35,X36
[shift_doc_tilt]001
X54=X34-X21
X55=X35-X22
SD X0,X0,X52,X54,X55
[alignment_doc]001
X91=X0
RT SQ
[tilted_images]{*****X91}
scr001
X52 ; rotation angle
X54,X55 ; x-, y-shift
; Apply a circular mask on the centrered images
ma
scr001
[aligned_tilted]{*****X91}
(43.)
g ; Gaussian cutoff
c ; background set to circumference average
x51,x51 ; mask center
(2.5) ; Gaussian falloff
LB4
; Compute average and variance maps
AS R
[aligned_tilted]*****
x63-x62
A
[tilted_avg]001
[tilted_var]001
;-----[ delete intermediate file
de
scr001
en d
;------------------------------------------------------------------------------!
; b07.fed/hbl : reads the eulerian angles and stores them in a doc file :
;------------------------------------------------------------------------------!
md
tr on
; SAMPLE INPUT FROM TILT_PARAM_DOC:
;
; ; hbl/hbl dcb001.hbl Tue Feb 13 17:18:19 2002
; TILTANGLE, AXIS DIR. IN: 0 DEG IM. THETA GAMMA PHI
; 0124 6 48.954857 -0.237597 -0.333951 0.000000 0.000000
; phi tilt dir tilt dir
; untilted tilted
;------------------------------------------------------------------------------!
; SAMPLE INPUT FROM ALIGN_DOC_UNTILT:
;
; theta & psi
;------------------------------------------------------------------------------!
;; ali/hbl 17-Feb-01 AT 21:34:26 ../doc/DAL004.hbl
; 1 4 149.07 0.67946 -0.47203
; 2 4 170.17 0.13753 -2.6509
; 3 4 189.85 -5.1422 -6.7959
; 4 4 109.70 -2.2350 -0.48043
; 5 4 70.323 3.7882 -1.6368
; PARAMETERS:
x40=124. ; index number for relevant line in TILT_PARAMS_DOC
X63=1. ; first image number
X62=76. ; last image number
; INPUTS:
fr l
[tilt_params_doc]../doc/dcb001 ; doc file containing tilt parameters
fr l
[align_doc_untilt]../doc/dalu ; untilted alignment doc filename template
; OUTPUT:
fr l
[angles_doc]../doc/dang ; Eulerian angle doc file template
; END BATCH HEADER
; Reads back the Eulerian angles theta and psi in your windowing doc file
; (this is how WEB stores it when you fit the angles during particle picking)
ud x40,x32,x31
[tilt_params_doc]
; Reads back the eulerian angles phi, corresponding to the in-plane rotation
; applied to untiled-specimen images during their alignment (b05.new)
do lb1 X10=x63,x62
ud ic x10,x33
[align_doc_untilt]001
x33=-x33 ; correct for sign convention
x33=x33-x31 ; subtract relative rotation between tilt pair
x34=0.0 ; dummy variable for Eulerian angle psi
; Stores the three eulerian angles psi, theta, & phi in a doc file
SD x0,x34,x32,x33
[angles_doc]001
lb1
;------------------------------------------------------------------------------!
; For clarity, we add or subtract 360 to angle phi so that its value is
; restricted between 0 ET 360 (it helps if you want to check angles)
;------------------------------------------------------------------------------!
; loop through
DO LB9 X70=1,4
X71=X70+1. ; counter for new ANGLES_DOC
; loop through particles
DO LB8 X10=x63,x62
; get old angles
UD S X10,X21,X22,X23
[angles_doc]{***x70}
; force phi to be between 0 and 360
IF(X23.GT.0.0)GOTO LB20
X23=X23+360.
LB20
IF(X23.LT.360)GOTO LB22
X23=X23-360.
LB22
SD X10,X21,X22,X23
[angles_doc]{***x71}
LB8
LB9
EN
;---------------------------------------------------------------------------! ; b08.fed/hbl : Multivariate Statsitical Analysis (MSA) on the aligned ; untilted-specimen images : ;---------------------------------------------------------------------------! md tr on ; PARAMETERS: X63=1. ; first image number X62=76. ; last image number x25=0.2 ; additive constant, in case there are pixel values<0 ; INPUTS: fr l [untilted_avg]../r2d/avgu ; untilted centered average filename template fr l [aligned_untilt]../images/cenu ; untilted aligned image filename template ; OUTPUTS: fr l [final_mask]../r2d/mask01 ; binary mask / thresholded average fr l [coran]../r2d/coran1 ; prefix for correspondence analysis ; results files : ; coran1_SEQ.hbl ; coran1_IMC.hbl ; coran1_PIX.hbl ; coran1_EIG.hbl fr l [ps_map]../r2d/map.ps ; postscript eigenvalue map ; END BATCH HEADER ;---------------------------------------------------------------------------! ; compute a spherical mask : mo [final_mask] 100,100 c 43. ; compute the contingency table (or sequential file) SEQ001.hbl : ca s [aligned_untilt]***** X63-X62 [final_mask] 7 c x25 ; additive constant* [coran] ; ; Computes the projection map corresponding to axes 1 and 2 ca sm ; correspondance analysis, show map and eigenvalues i ; each _i_mage is represented by a vector in n-dimensional space [coran] ; coordinate file prefix 1 ; number of horizontal patches 1,2 ; eigenvectors to map s ; represent by a _s_ymbol + ; symbol Y ; prepare postscript map 3.0 ; range, measured in standard deviations [ps_map] 12,12 0 0 ; The 8 blank lines above are used in CA SME as acceptance of default values. en
;---------------------------------------------------------------------------!
; b09.fed/hbl : Explore the tendencies expressed by factorial axes 1 to 7
; Creates montages MIMP001.hbl and MREC001.hbl
;---------------------------------------------------------------------------!
md
tr on
; INPUTS:
fr l
[coran]../r2d/coran1 ; prefix for correspondence analysis
; results files :
; coran1_SEQ.hbl
; coran1_IMC.hbl
; coran1_PIX.hbl
; coran1_EIG.hbl
x81=1 ;first image number
x82=76 ;last image number
; OUTPUTS:
fr l
[importance_montage]../r2d/MIMP001 ; montage of importance images
fr l
[reconstituted_montage]../r2d/MREC001 ; montage of reconstituted images
; TEMPORARY FILES:
fr l
[importance_img]../r2d/imp ; importance image filename template
fr l
[reconstituted_img]../r2d/rec ; reconstituted image filename template
; END BATCH HEADER
x11=100. ; initialize importance image file # for negative-most eigenvalue
x21=100. ; initialize reconstituted image file # for negative-most eigenvalue
; loop through eigenvectors
do lb1 x10=1,7
; importance images of (-) & (+) extremities along axes 1 to 7
x11=x11+1. ; increment file number for negative-most eigenvalue
x12=x11+1. ; increment file number for positive-most eigenvalue
sd c
[coran]
x10 ; factorial axis to be used
tempdoc1
sd s
tempdoc1
x81,x82
(1)
tempdoc{***x10}
ud x81,x83
tempdoc{***x10}
CA SRD
[coran] ; correspondence analysis results files prefix
x83 ; file number
x10 ; factorial axis to be used
tmp***
cp
tmp{***x83}
[importance_img]{***x11} ; output importance image
ud x82,x84
tempdoc{***x10}
CA SRD
[coran] ; correspondence analysis results files prefix
x84 ; file number
x10 ; factorial axis to be used
tmp***
cp
tmp{***x84}
[importance_img]{***x12} ; output importance image
ud ice
tempdoc2
de
tempdoc1
de
tmp{***x83}
de
tmp{***x84}
x11=x12
; reconstitution images of (-) & (+) extremities along axes 1 to 7
x21=x21+1. ; increment file number for negative-most eigenvalue
x22=x21+1. ; increment file number for positive-most eigenvalue
CA SRA
[coran] ; correspondence analysis results files prefix
x10 ; factorial axis to be used
(-0.2) ; eigenvalue for second file
[reconstituted_img]{***x21} ; output importance image
CA SRA
[coran] ; correspondence analysis results files prefix
x10 ; factorial axis to be used
(0.2) ; eigenvalue for second file
[reconstituted_img]{***x22} ; output importance image
x21=x22
lb1
; montages of importance and reconstitution images
mn s
[importance_img]***
102,104,106,108,110,112,114,101,103,105,107,109,111,113
7,2 ; images per row, margin width
2 ; margin value
[importance_montage]
mn s
[reconstituted_img]***
102,104,106,108,110,112,114,101,103,105,107,109,111,113
7,2 ; images per row, margin width
2 ; margin value
[reconstituted_montage]
; delete intermediate files :
de a
[importance_img]101
de a
[reconstituted_img]101
de a
tempdoc001
en d
;---------------------------------------------------------------------------!
; b10.fed/hbl : Hierarchical Ascendant Classification (HAC) after the MSA :
;---------------------------------------------------------------------------!
md
tr on
; PARAMETERS:
x10=1.0 ; test value to jump ahead (1.) or not (0.0)
x26=112 ; maximum dendrogram branch point
x27=1 ; cutoff for branch points
; INPUTS:
fr l
[image_coordinates]../r2d/coran1_IMC ; (implicit) image coordinates
fr l
[dendro_doc]../doc/dhac001 ; dendrogram doc file (interactive session)
fr l
[aligned_untilt]../images/cenu ; untilted aligned image filename template
; OUTPUTS:
fr l
[ps_dendrogram]../r2d/psdndplot ; PostScript, truncated dendrogram plot
fr l
[class_count_doc]../doc/dcount001 ; doc file with number of images per class
fr l
[class_select_doc]../doc/dcla ; class selection doc filename template
fr l
[class_avg]../r2d/clavg ; class average filename template
fr l
[class_var]../r2d/clvar ; class variance filename template
fr l
[class_avg_montage]../r2d/mclavg001 ; class average montage
fr l
[class_var_montage]../r2d/mclvar001 ; class variance montage
; END BATCH HEADER
if(x10.eq.1.0) goto lb19
;********************************************************************
; I RECOMMEND DOING THIS PART INTERACTIVELY -- SAVE THE RESULTS FILE
;********************************************************************
; Runs classification and creates dendrogram doc file
cl hc
[image_coordinates]
1-7 ; eigenvectors to use
0 ; eigenvector weighting ('0'-->all 1's)
5 ; clustering criterion: Ward's method
n ; postscript file? (we'll make a truncated one later)
y ; dendrogram doc file?
[dendro_doc]
en
(Check the dendrogram shape in results file and note Max and min values)
lb19
; Starts again HAC and creates dendrogram file DEND001.hbl
; In my case I used a threshold value of 3 for a max value of 203
cl hc
[image_coordinates]
1-7 ; eigenvectors to use
0 ; eigenvector weighting ('0'-->all 1's)
5 ; clustering criterion: Ward's method
t ; _t_runcated postscript file
x27 ; cutoff
[ps_dendrogram]
n
; Compute the number of images per class
x11=x27/x26 ; branch cutoff divided by maximum branch point
cl hd ; hierarchical classification, calculate classes
x11
[dendro_doc]
[class_count_doc]
; Creating doc files containing the image liste for each class
cl he
x11
[dendro_doc]
[class_select_doc]***
; Compute average and variance maps for each class
do lb1 x10=1,4
as dc
[aligned_untilt]*****
[class_select_doc]{***x10}
a ; sum _all_images
[class_avg]{***x10}
[class_var]{***x10}
lb1
; Creates montage files of average and variance maps
mn s
[class_avg]***
1-4 ; file numbers
4,2 ; images per row, margin width
2 ; margin value
[class_avg_montage]
mn s
[class_var]***
1-4 ; file numbers
4,2 ; images per row, margin width
2 ; margin value
[class_var_montage]
en
;---------------------------------------------------------------------------!
; b11.fed/hbl : Creating symmetry document files taking into account
; the D6 point-group symmetry of Lumbricus hemoglobin :
;---------------------------------------------------------------------------!
md
tr on
; OUTPUTS:
fr l
[top_sym]../doc/d6top ; top-view symmetry doc file
fr l
[side_sym]../doc/d6side ; side-view symmetry doc file
; END BATCH HEADER
; D6 Symmetry for hexagonal top views
; 6-fold axis parallel to Z axis)
do lb1 x10=1,12
rr x11
0.0,0.0,0.0,0.0,0.0,0.0,0.0,60.,120.,180.,240.,300.
rr x12
0.0,0.0,0.0,0.0,0.0,0.0,180.,180.,180.,180.,180.,180.
rr x13
0.0,60.,120.,180.,240.,300.,0.0,0.0,0.0,0.0,0.0,0.0
sd x10,x13,x12,x11
[top_sym]
lb1
; D6 Symmetry for rectangular side views
; (6-fold axis parallel to Y axis)
do lb2 x20=1,12
rr x11
0.0,0.0,0.0,0.0,0.0,0.0,180.0,180.0,180.0,180.,180.,180.
rr x12
0.0,60.0,120.,180.,240.,300.,0.0,60.,120.,180.,240.,300.
rr x13
0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
sd x20,x13,x12,x11
[side_sym]
lb2
en d
;fed/hbl 21-AUG-2006 AT 18:05:50 ../doc/d6top.hbl
1 3 0.0000 0.0000 0.0000
2 3 60.000 0.0000 0.0000
3 3 120.00 0.0000 0.0000
4 3 180.00 0.0000 0.0000
5 3 240.00 0.0000 0.0000
6 3 300.00 0.0000 0.0000
7 3 0.0000 180.00 0.0000
8 3 0.0000 180.00 60.000
9 3 0.0000 180.00 120.00
10 3 0.0000 180.00 180.00
11 3 0.0000 180.00 240.00
12 3 0.0000 180.00 300.00
;fed/hbl 21-AUG-2006 AT 18:05:50 ../doc/d6side.hbl
1 3 0.0000 0.0000 0.0000
2 3 0.0000 60.000 0.0000
3 3 0.0000 120.00 0.0000
4 3 0.0000 180.00 0.0000
5 3 0.0000 240.00 0.0000
6 3 0.0000 300.00 0.0000
7 3 0.0000 0.0000 180.00
8 3 0.0000 60.000 180.00
9 3 0.0000 120.00 180.00
10 3 0.0000 180.00 180.00
11 3 0.0000 240.00 180.00
12 3 0.0000 300.00 180.00
;------------------------------------------------------------------------------! ; b12.fed/hbl : 3D Reconstruction from the tilted-speci;en images ; corresponding to the three image classes obtained from MSA : ;------------------------------------------------------------------------------! md tr on ; NOTE: ; Make sure that the view of the untilted class numbers in this batch file ; are the ones you want, and that they correspond to the correct symmetry file. ; For example, untilted class average #4 may not be the end-on view in your ; own image set ; INPUTS: fr l [aligned_tilted]../images/cent ; tilted aligned tilted image filename template fr l [class_select_doc]../doc/dcla ; class selection doc filename template fr l [angles_doc]../doc/dang ; Eulerian angle doc file template fr l [side_sym]../doc/d6side ; side-view symmetry doc file fr l [top_sym]../doc/d6top ; top-view symmetry doc file ; OUTPUTS: fr l [class_vol]../r3d/vcla ; class volume filename template ; END BATCH HEADER ; 3D Reconstruction of image class No.1 : bp rp [aligned_tilted]0**** [class_select_doc]001 47.0 ; object radius [angles_doc]005 [side_sym] [class_vol]001 0.15e-04,0 ; correction weight, correction limit 50,1 ; iteration limit, mode 1 (smoothing) 0.0,2.00 ; minimum, maximum values in projections 0.999 ; smoothing constant ; 3D Reconstruction of image class No.3 : bp rp [aligned_tilted]0**** [class_select_doc]003 47.0 ; object radius [angles_doc]005 [side_sym] [class_vol]003 0.15e-04,0 ; correction weight, correction limit 50,1 ; iteration limit, mode 1 (smoothing) 0.0,2.00 ; minimum, maximum values in projections 0.999 ; smoothing constant ; 3D Reconstruction of image class No.4 : bp rp [aligned_tilted]0**** [class_select_doc]004 47.0 ; object radius [angles_doc]005 [top_sym] [class_vol]004 0.15e-04,0 ; correction weight, correction limit 50,1 ; iteration limit, mode 1 (smoothing) 0.0,2.00 ; minimum, maximum values in projections 0.999 ; smoothing constant ;----------------------------------------------------------------------! ; REMARK : You might want to speed up the reconstruction. ; if bp rp to slow on your computer, you can also try operation "BP 3F" ;----------------------------------------------------------------------! ;bp 3f ;[aligned_tilted]0**** ;[class_select_doc]001 ;[angles_doc]005 ;[side_sym] ;[class_vol]001 ;; ;bp 3f ;[aligned_tilted]0**** ;[class_select_doc]003 ;[angles_doc]005 ;[side_sym] ;[class_vol]003 ;; ;bp 3f ;[aligned_tilted]0**** ;[class_select_doc]004 ;[angles_doc]005 ;[top_sym] ;[class_vol]004 ;; en d
;------------------------------------------------------------------------------!
; b13.fed/hbl : Finding a common orientation for the three reconstructions :
; 2D projection of the volumes along axis Z
; Rotation of side view volumes by 90 degrees around X axis
; 2D projection of the rotated side view volumes
;------------------------------------------------------------------------------!
md
tr on
; NOTE:
; This batch file uses classes 1, 3, and 4.
; INPUTS:
fr l
[class_vol]../r3d/vcla ; class volume filename template
; OUTPUTS:
fr l
[prj_montage]../r3d/mpro ; projection montage filename template
; END BATCH HEADER
;------------------------------------------------------------------------------!
; Projection of the three reconstruction volumes
pj 3
[class_vol]001
100 ; dimension
scr001
0,0,0 ; projection angles
pj 3
[class_vol]003
100
scr003
0,0,0 ; projection angles
pj 3
[class_vol]004
100
scr004
0,0,0
; montage of the 3 projections
mn s
scr***
1,3,4
3,2
2.
[prj_montage]001
; rotating the two side view volumes by 90 degrees around X axis
rt 3d
[class_vol]001
ttt001
90.0,90.0,-90.0
rt 3d
[class_vol]003
ttt003
90.0,90.0,-90.0
; 2D Projection of the three reconstruction volumes after rotation
pj 3
ttt001
100
scr011
0,0,0
pj 3
ttt003
100
scr013
0,0,0
; montage of the 3 new projections
mn s
scr***
11,13,4
3,2
2.
[prj_montage]002
; rotating VCLA003 by 90 degrees around X and 30 degrees around Z
rt 3d
[class_vol]003
ttt003
90.0,90.0,-60.0
pj 3
ttt003
100
scr013
0,0,0
; montage of the 3 new projections
mn s
scr***
11,13,4
3,2
2.
[prj_montage]003
; clean up
de a
scr001
de a
scr011
de
ttt001
de
ttt003
en d
;--------------------------------------------------------------------------!
; b14.fed/hbl : More general approach for the reorientation of the volumes
; using a stochastic approach, using "OR 3Q" operation :
; This test uses the hexagonal top view volume as reference
;--------------------------------------------------------------------------!
; NOTE:
; By default, this batch file assumes [class_vol]004 is the reference, top view,
; and aligns [class_vol]'s 001 and 003 to it.
; INPUTS:
fr l
[class_vol]../r3d/vcla ; class volume filename template
; OUTPUT:
fr l
[vol_align_doc]../doc/dalv001 ; volume alignment doc filename template
; END BATCH HEADER
md
tr on
; search best 3D alignment of VCLAx20 on VCLA004 using a starting
; position of : phi = 90, theta = 90, and psi = -90
x20=1. ; class volume # to align
or 3q x21,x22,x23,x24
[class_vol]004
[class_vol]{***x20}
41 ; radius
90.0,90.0
-90.0
sd x20,x21,x22,x23,x24
[vol_align_doc]
; search best 3D alignment of VCLAx20 on VCLA004 using a starting
; position of : phi = 90, theta = 90, and psi = -60
x20=3. ; class volume # to align
or 3q x21,x22,x23,x24
[class_vol]004
[class_vol]{***x20}
41
90.0,90.0
-60.0
sd x20,x21,x22,x23,x24
[vol_align_doc]
en
;fed/hbl 21-AUG-2006 AT 18:59:26 ../doc/dalv001.hbl
1 4 90.000 89.999 -90.000 0.89578
3 4 90.000 89.998 -59.978 0.89503
;--------------------------------------------------------------------------!
; b15.fed/hbl : merging of the three conical tilt series in a single group
; after modifying the eulerian angles of each image accordingly
; Finally computation of a "multi-cone" or "merged" 3D
; reconstruction volume (devoid of the missing cone artifact)
;--------------------------------------------------------------------------!
; volume of class #4 phi = 0.0, theta = 0.0, psi = 0.0
; volume of class #1 phi = 90., theta = 90., psi = -90.
; volume of class #3 phi = 90., theta = 90., psi = -60.
; If these aren't the values you want, change the batch file below.
;INPUTS:
fr l
[class_count_doc]../doc/dcount001 ; doc file with number of images per class
fr l
[angles_doc]../doc/dang ; Eulerian angle doc file template
fr l
[class_select_doc]../doc/dcla ; class selection doc filename template
fr l
[aligned_tilted]../images/cent ; tilted aligned tilted image filename template
fr l
[top_sym]../doc/d6top ; top-view symmetry doc file
;OUTPUTS:
fr l
[merged_angles_doc]../doc/dang010 ; merged angles doc file
fr l
[merged_select_doc]../doc/dsel001 ; merged selectoin doc file
fr l
[merged_vol]../r3d/vtot001 ; merged volume
;TEMPORARY FILE:
;dint***
;--------------------------------------------------------------------------!
md
tr on
; Reads the class number and the Eulerian rotation angles applied
; to reorient the corresponding volume :
do lb1 x50=1,3
; (In the following read-register commands, there are fewer registers named
; than there are numbers in the following line. What this means is that, in
; each cycle of the do-loop, the next number will be assigned to that register.
;
rr x11
4.,1.,3.
; phi, one for each volume
rr x51
0.0,90.0,90.0
; theta, one for each volume
rr x52
0.0,90.0,90.0
; psi, one for each volume
rr x53
0.0,-90.,-60.
; reads back the number of images per class
ud x11,x12
[class_count_doc]
; Modify the original eulerian angles of the tilted-specimen images
; by applying the phi, theta, psi rotation angles, using "VO RA"
vo ra
[angles_doc]005
x53,x52 ; psi, theta
x51 ; phi
dint{***x11} ; temporary file
; Internal DO loop for each image class
do lb3 x60=1,x12
x10=x10+1.0
ud x60,x20
[class_select_doc]{***x11}
; Copy the tilted-specimen images of the three classe with
; consecutive and increasing numbers 1, 2, 3, etc.. 71, 72.
cp
[aligned_tilted]{*****x20}
[aligned_tilted]1{****x10}
; Creates the corresponding new eulerian angular doc file
ud x20,x21,x22,x23
dint{***x11}
sd x10,x21,x22,x23
[merged_angles_doc]
; Creates a new selection doc file containing the image numbers
sd x10,x10
[merged_select_doc]
lb3
de
dint{***x11}
lb1
;--------------------------------------------------------------------------!
;-----[ 3D Reconstruction from the merged 3 image classes : VTOT001.hbl
;--------------------------------------------------------------------------!
bp rp
[aligned_tilted]1****
[merged_select_doc]
47.0 ; radius
[merged_angles_doc]
[top_sym]
[merged_vol]
0.15e-04,0 ; correction weight (lambda), correction limit
50,1 ; iteration limit, mode (1=smoothing)
-5.0,5.0 ; min., max. values in 2D data set
0.999 ; smoothing constant
;--------------------------------------------------------------------------!
;if "bp rp" too slow, use operation "bp 3f" :
;--------------------------------------------------------------------------!
;bp 3f
;[aligned_tilted]1****
;[merged_select_doc]
;[merged_angles_doc]
;[top_sym]
;[merged_vol]
;
en
;---------------------------------------------------------------------------!
; b16.fed/hbl : Renames .hbl files for web viewing, in case the ".DAT" bug
; would still remain in your version of Web software.
;---------------------------------------------------------------------------!
md
tr on
do lb1 x10=1,76
vm
cp ../images/cenu{*****x10}.hbl ../images/cenu{*****x10}.DAT
lb1
vm
cp ../doc/dhac001.hbl ../doc/dhac001.hbl.DAT
en d
;fed/hbl 21-AUG-2006 AT 18:59:37 ../doc/dang010.hbl
1 3 0.0000 47.941 129.58
2 3 0.0000 47.941 39.550
3 3 0.0000 47.941 129.90
4 3 0.0000 47.941 219.52
5 3 0.0000 47.941 59.720
6 3 0.0000 47.941 49.600
7 3 0.0000 47.941 49.650
8 3 0.0000 47.941 139.74
9 3 0.0000 47.941 29.660
10 3 0.0000 47.941 119.71
11 3 0.0000 47.941 239.85
12 3 0.0000 47.941 149.62
13 3 0.0000 47.941 209.77
14 3 0.0000 47.941 119.75
15 3 0.0000 47.941 79.810
16 3 0.0000 47.941 339.87
17 3 0.0000 47.941 339.72
18 3 0.0000 47.941 19.680
19 3 0.0000 47.941 349.51
20 3 0.0000 47.941 99.680
21 3 0.0000 47.941 79.740
22 3 0.0000 47.941 339.85
23 3 0.0000 47.941 79.710
24 3 0.0000 47.941 69.650
25 3 0.0000 47.941 349.70
26 3 0.0000 47.941 189.79
27 3 0.0000 47.941 109.69
28 3 0.0000 47.941 9.6600
29 3 0.0000 47.941 19.810
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50 3 82.929 97.769 317.46
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57 3 248.33 67.746 196.37
58 3 110.78 68.535 283.96
59 3 290.91 111.58 196.09
60 3 128.10 55.634 275.75
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69 3 82.813 97.894 287.44
70 3 96.512 82.836 287.53
71 3 331.04 134.12 218.93
72 3 207.94 45.604 219.64
;fed/hbl 21-AUG-2006 AT 18:59:37 ../doc/dsel001.hbl
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