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Last modified: 13.07.2004
(See /IDL/pro_src/RODENA/pro/misc/coor2ind.pro)
(See /IDL/pro_src/RODENA/pro/misc/cw_defroi.pro)
(See /IDL/pro_src/RODENA/pro/misc/d3show_tc.pro)
(See /IDL/pro_src/RODENA/pro/misc/d3l_n.pro)
(See /IDL/pro_src/RODENA/pro/misc/d3show.pro)
(See /IDL/pro_src/RODENA/pro/misc/d3s_n.pro)
(See /IDL/pro_src/RODENA/pro/misc/find_f.pro)
(See /IDL/pro_src/RODENA/pro/misc/gen_dm.pro)
(See /IDL/pro_src/RODENA/pro/misc/image_cont_2.pro)
(See /IDL/pro_src/RODENA/pro/misc/ind2coor.pro)
(See /IDL/pro_src/RODENA/pro/misc/label_size.pro)
(See /IDL/pro_src/RODENA/pro/misc/label_ws.pro)
(See /IDL/pro_src/RODENA/pro/misc/main.pro)
(See /IDL/pro_src/RODENA/pro/misc/mst.pro)
(See /IDL/pro_src/RODENA/pro/misc/nng.pro)
(See /IDL/pro_src/RODENA/pro/misc/plot_dna.pro)
(See /IDL/pro_src/RODENA/pro/misc/slide_image.pro)
(See /IDL/pro_src/RODENA/pro/misc/slide_image_tc.pro)
(See /IDL/pro_src/RODENA/pro/misc/strparse.pro)
(See /IDL/pro_src/RODENA/pro/misc/trace.pro)
(See /IDL/pro_src/RODENA/pro/misc/vol_tiff_read.pro)
(See /IDL/pro_src/RODENA/pro/misc/wd3d.pro)
(See /IDL/pro_src/RODENA/pro/misc/wd3d_contin.pro)
(See /IDL/pro_src/RODENA/pro/misc/wd3d_merge.pro)
(See /IDL/pro_src/RODENA/pro/misc/write_s_ascii.pro)
List of Routines
Routine Descriptions
COOR2IND
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NAME:
COOR2IND
PURPOSE:
calculates coordinates into an index
CATEGORY:
CALLING SEQUENCE:
ind = coor2ind(vec, siz)
INPUTS:
vec: coordinate array
siz: array size from size(arr)
OUTPUTS:
ind: index of coordinate array
RESTRICTIONS:
Only for 1 to 3 dim. arrays.
PROCEDURE:
EXAMPLE:
a=bytarr(64,64,64)
print,coor2ind([32,32,32], size(a))
133152
MODIFICATION HISTORY:
Mon Jul 21 11:50:17 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
CW_DEFROI
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NAME:
CW_DEFROI
PURPOSE:
Widget to define a region of interest within a widget drawable.
CATEGORY:
Regions of interest, graphics.
CALLING SEQUENCE:
Result = CW_DEFROI(draw)
INPUTS:
Draw = id of drawable to draw the region. The drawable should
have both MOTION and BUTTON events enabled.
KEYWORD PARAMETERS:
IMAGE_SIZE = the size of the underlying array, expressed
as a two element vector: [columns, rows]. Default =
drawable size / zoom.
OFFSET = offset of lower left corner of image within the
drawable. Default = [0,0].
ORDER = if set, return inverted subscripts, as if the array
were output from top to bottom.
RESTORE = Set to restore the drawable to its previous appearance
on exit. Otherwise, the regions remain on the drawable.
ZOOM = if the image array was expanded (via REBIN for example)
specify this two element vector containing the expansion
factor in X and Y. Default = [1,1]. Must be integer.
START_MODE = 0 POLYGON (default)
= 1 POINT
= 2 RECTANGLE
= 3 CIRCLE
= 10 POLY LINE
OUTPUTS:
Result = subscripts of points within the region[s] defined.
If no region was defined, a scalar -1 is returned.
COMMON BLOCKS:
None.
SIDE EFFECTS:
The regions are drawn within the drawable. Set the RESTORE
keyword to undo the damage.
RESTRICTIONS:
This is a MODAL widget. No other widget applications will be
responsive while this widget is in use.
PROCEDURE:
Complicated.
EXAMPLE:
To obtain the average of the counts of a region within a drawable:
Assume A = the array of interest, n columns, m rows, and that
it is displayed in drawable D, at offset X=20, Y=100, and zoomed
with a factor of 2:
TV, REBIN(A, M*2, N*2), 20, 100 ;Display the image
q = CW_DEFROI(D, ZOOM=[2,2], OFFSET=[20,100], IMAGE_SIZE=[m,n])
if q(0) ne -1 then print,'Average = ', total(a(q))/n_elements(q)
MODIFICATION HISTORY:
DMS, RSI, December, 1993. Written.
D2SHOW_TC
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NAME:
d2show_tc
function d3show_tc,vol,ZOOM=zom,WINDOWS=winno,_EXTRA=extr
sa=size(vol)
dim=ceil(sqrt(sa(4)))
if not keyword_set(zom) then zom=1
b=bytarr(sa(1),sa(2)*dim*zom,sa(3)*dim*zom)
for i=0,sa(4)-1 do begin
x=sa(2)*zom*(i mod dim)
y=sa(3)*zom*(i/dim)
if zom gt 1 then $
b(*,x:x+sa(2)*zom-1,y:y+sa(3)*zom-1)= $
rebin(vol(*,*,*,i),3,sa(2)*zom,sa(3)*zom,/sa) $
else b(*,x:x+sa(2)-1,y:y+sa(3)-1)=vol(*,*,*,i)
endfor
slide_image_tc,b,top_id=wsl,slide_window=sw,full_window=fw,_extra=extr
winno=[fw,sw]
return,wsl
end
D3L_N
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NAME:
D3L_N
PURPOSE:
Input of 3d-images from sequences of section tif-files and definition of
data arrays in common wd3d_dat as preparation od call WD3D.
File sequences have to be in the form xxxxxyyy.zzz where xxxxx is an arbitrary
string, yyy a number, starting from NUMBER_FIELD and zzz an arbitrary string
according EXTENSION
CATEGORY:
3d image analysis
CALLING SEQUENCE:
d3n
INPUTS:
none
OPTIONAL INPUTS:
none
KEYWORD PARAMETERS:
OVER_COLOR: Pseudocolor display is used.
If !version.arch eq 'mipseb' normally truecolor is used
PATH: path For pickfile path is used as beging search path ['/']
NAME: name Full file sequence specification, no pickfile is used.
e.g. '/mnt/iliad/series/abcd???.tif'
NOTOPHAT: Blue channel is not overwritten by top-hat-transformation
NUMBER_FIELD: sele_n A string describing the first section image ['000']
e.g. '27'
NUMBER_SECTIONS:anz_sec Number of images to be read in starting from NUMBER_FIELD
[all found]
EXTENSION: sele_e A string describing the extension ['tif']
RESULT: err Returns an error value (0 an error occured)
LABEL: Space for label image is allocated
NAM_LABEL: nlabe Name of labelled image sequence
SIZE_TOPHAT: itophat_size Size of top-hat-transformation [3]
SIZE_OPENING: iopen_size Size of opening [1]
Extra keywords used from wd3d, not used from d3l_n, only transferred to wd3d
(see WD3D)
XVISIBLE: ixvis
YVISIBLE: iyvis
NOSIGNAL_COUNT:
MIN_SIGNAL_VOLUME:imin_sig_vol
MIN_NUCLEUS_VOLUME:imin_nuc_vol
THRESH_TOPHAT: itophat_thr
NOGALLERY:
BOX_ALL:
VERBOSE:
OUTPUTS:
OPTIONAL OUTPUTS:
COMMON BLOCKS:
VOLUME_DATA: for possible use of SLICER procedure
WD3D_DAT: contains all volume data
a: color volume (pseudo color [x,y,z], truecolor [3,x,y,z]
rh,fl,bl:red, green, blue channel (bl is overwritten by top-hat
lrh,lfl:label images
rv,gv,bv:look-up-tables
sa: size of volume [x,y,z]
color: true if color volume
true_color:true if truecolor display
iname: name selector string
jname: automatic generated filename for results
ipath: path
lname: label file selector string
clsm: Zeiss header from first tif-file read
x_sp,y_sp,z_sp:Pixel sizes from Zeiss header
SIDE EFFECTS:
RESTRICTIONS:
Use of procedure vol_tiff_read
PROCEDURE:
EXAMPLE:
MODIFICATION HISTORY:
Fri Jul 11 09:30:28 1997, Karsten Rodenacker
Wed Jul 30 09:23:36 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
D3SHOW
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NAME:
d3show
function d3show,vol,ZOOM=zom,WINDOWS=winno,_EXTRA=extr
sa=size(vol)
dim=ceil(sqrt(sa(3)))
if not keyword_set(zom) then zom=1
b=bytarr(sa(1)*dim*zom,sa(2)*dim*zom)
for i=0,sa(3)-1 do begin
x=sa(1)*zom*(i mod dim)
y=sa(2)*zom*(i/dim)
if zom gt 1 then $
b(x:x+sa(1)*zom-1,y:y+sa(2)*zom-1)=rebin(vol(*,*,i),sa(1)*zom,sa(2)*zom,/sa) $
else b(x:x+sa(1)-1,y:y+sa(2)-1)=vol(*,*,i)
endfor
slide_image,b,top_id=wsl,slide_window=sw,full_window=fw,_extra=extr
winno=[fw,sw]
return,wsl
end
D3S_N
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NAME:
D3S_N
Speichern von 3D Daten fuer WD3D
Keywords:
NUMBER_FIELD: Laufnummer fuer ersten Schnitt ('000')
NUMBER_SECTIONS:Anzahl Schnitte (0) all
EXTENSION: Extension ('tif')
NAME: Name der Sequence (complete)
LABEL: Label images are stored (lrh,lfl,bl)
FIND_F
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NAME:
FIND_F
PURPOSE:
Find first element in a byte array of whose value
reflects the condition and value.
Search starts from init index.
The function returns the index of the found element.
For large arrays, e.g. [256,256,64] idl function where is to slow.
CATEGORY:
Utility
CALLING SEQUENCE:
ind = find_f(arr, init, condition=cond, value=val)
INPUTS:
arr: Byte array to be searched
init: Long initial index
KEYWORD PARAMETERS:
CONDITION: A number reflecting the used condition [def. 0]
0 -> EQ (! !=)
1 -> NE (! ==)
2 -> GE (! <)
3 -> LE (! >)
4 -> GT (! <=)
5 -> LT (! >=)
VALUE: compared value [def. 0B]
OUTPUTS:
index of found array element
-1 not found from starting index to end of array
-2 not a byte array
-3 start index not in array
SIDE EFFECTS:
call_external to sharable library rod_share[.exe/.dll/.so] with
entry point find_first_b.
RESTRICTIONS:
Only implemented for vms, hp-ux, IRIX and Win32 !version.os
PROCEDURE:
Related procedures: coor2ind, ind2coor
EXAMPLE:
a=bytarr(64,64,64)
a[32,32,32]=25b
ind=find_f(arr,0,cond=2,val=25)
print,ind, ind2coor(ind, size(a))
133152 32 32 32
MODIFICATION HISTORY:
Mon Jul 21 11:00:56 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
GEN_DM
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NAME:
GEN_DM
Distanzmatrix berechnen
FUNCTION GEN_DM,x,y,MAINMAX=mm
sx=size(x)
sy=size(y)
w=where(sx ne sy,cw)
if cw ne 0 then message,'Pointvectors differ'
if sx(0) ne 1 then message,'Pointvectors not 1-dim.'
dm=fltarr(sx(1),sx(1))
for i=0,sx(1)-1 do for j=i,sx(1)-1 do begin
dm(i,j)=norm([x(i),y(i)]-[x(j),y(j)])
dm(j,i)=dm(i,j)
endfor
if keyword_set(mm) then begin
maxi=max(dm)+1.
for i=0,sx(1)-1 do dm(i,i)=maxi
endif
return,dm
end
IMAGE_CONT_2
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NAME:
IMAGE_CONT_2
PURPOSE:
Overlay an image and a contour plot.
CATEGORY:
General graphics.
CALLING SEQUENCE:
IMAGE_CONT_2, A, B
INPUTS:
A: The two-dimensional array to display with TV.
A: The 2nd two-dimensional array to display with CONTOUR.
KEYWORD PARAMETERS:
WINDOW_SCALE: Set this keyword to scale the window size to the image size.
Otherwise, the image size is scaled to the window size.
This keyword is ignored when outputting to devices with
scalable pixels (e.g., PostScript).
ASPECT: Set this keyword to retain the image's aspect ratio.
Square pixels are assumed. If WINDOW_SCALE is set, the
aspect ratio is automatically retained.
INTERP: If this keyword is set, bilinear interpolation is used if
the image is resized.
OUTPUTS:
No explicit outputs.
COMMON BLOCKS:
None.
SIDE EFFECTS:
The currently selected display is affected.
RESTRICTIONS:
None.
PROCEDURE:
If the device has scalable pixels, then the image is written over
the plot window.
MODIFICATION HISTORY:
DMS, May, 1988.
IND2COOR
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NAME:
IND2COOR
PURPOSE:
calculates an index into coordinates
CATEGORY:
Utility
CALLING SEQUENCE:
arr = ind2coor(ind, siz)
INPUTS:
ind: index
siz: array size from size(xxx)
OUTPUTS:
arr: coordinates array
RESTRICTIONS:
Only for 1 to 3 dim arrays
PROCEDURE:
EXAMPLE:
help,ind2coor(123456,size(bytarr(64,64,64)))
<Expression> LONG = Array[3]
print,ind2coor(123456,size(bytarr(64,64,64)))
0 9 30
MODIFICATION HISTORY:
Mon Jul 21 11:52:59 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
LABEL_SIZE
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NAME:
LABEL_SIZE
PURPOSE:
Delete all objects from a label image with number of
pixels/voxels lt min_size and ge max_size and renumber the
labels consecutively.
Nothing is done if no object is found.
CATEGORY:
image processing / utilities
CALLING SEQUENCE:
label_size, lab, min_size[, max_size]
INPUTS:
lab: label image from label_region or label_ws
OPTIONAL INPUTS:
none
KEYWORD PARAMETERS:
none
OUTPUTS:
input image lab is changed
OPTIONAL OUTPUTS:
none
COMMON BLOCKS:
none
SIDE EFFECTS:
input image is changed
RESTRICTIONS:
PROCEDURE:
histogram, reverse_i is used to estimate objects
EXAMPLE:
MODIFICATION HISTORY:
Tue Aug 5 14:26:47 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
LABEL_WS
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NAME:
LABEL_WS
PURPOSE:
Labelling of all objects in an image or a volume with
watershed algorithm
CATEGORY:
Image processing
CALLING SEQUENCE:
lab = label_ws(img)
INPUTS:
img: binary image or volume
OPTIONAL INPUTS:
none
KEYWORD PARAMETERS:
LONG: Result is an integer array (def. byte)
For images with more than 255 objects.
MASK: Dilated input is used as mask parameter to reduces
computing time, good for small connected objects
REVERSE_INDEX: Variable which will contain the indices of the
reverse index list used by watershed, implicitly this
is the region processed. See in HISTOGRAM for explanation.
OUTPUTS:
lab: Label image
SIDE EFFECTS:
RESTRICTIONS:
The external function c_watershed is implicitly called by the
function tm_wshe2.
Application of watershed implies that background cannot be labelled!
PROCEDURE:
tm_wshe2 is applied on the inverted and binarized input image.
The resulting label image is multiplied by the binarized input
image.
If mask is set, tm_wshe2 is called with keyword MASK
containing the binarized input image dilated by a radius of
2. This will reduce computing time if the number of
pixels/voxels set is small against the size of the
image/volume. This is normally the case.
EXAMPLE:
xxx=bytarr(512,512) & xxx[32:34,32:34]=1 & xxx[62:64,62:64]=1
yyy=label_ws(xxx,/mask)
print, yyy[32,32], yyy[62,62]
1 2
MODIFICATION HISTORY:
Tue Aug 5 09:20:16 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
Mon Aug 4 14:12:49 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
MAIN
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NAME:
MAIN
PURPOSE:
Simple call interface for 3D inspection and analysis program WD3D
Calls D3L_N for loading volumes and then WD3D
CATEGORY:
3d-image analysis
CALLING SEQUENCE:
main
INPUTS:
OPTIONAL INPUTS:
KEYWORD PARAMETERS:
see D3L_N and WD3D
NOTOPHAT: -> Blue channel if any will be displayed
However the same channel is used for box marking too
LOAD_ONLY: -> The selected sequence will be loaded only
and the program returns to prompter
OVER: pseudo color
OUTPUTS:
OPTIONAL OUTPUTS:
COMMON BLOCKS:
see D3L_N and WD3D
SIDE EFFECTS:
Calls
D3L_N for loading image sequences
WD3D for interactive inspection and analysis
RESTRICTIONS:
PROCEDURE:
EXAMPLE:
main -> file choser starts from /
main,/PATH='/export/telepath/series/'
-> file choser starts from
/export/telepath/series/
MODIFICATION HISTORY:
Fri Jul 11 09:59:52 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
MST
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NAME:
MST
Minimum spanning tree bestimmen
FUNCTION MST,dm,ist
if n_params() lt 2 then ist=0
sdm=size(dm)
if sdm(0) ne 2 then message,'Distancematrix not 2-dim.'
if sdm(1) ne sdm(2) then message,'Distancematrix not a sqare'
n=sdm(1)
ss=bytarr(n) & ss(ist)=1b
aa=intarr(2,n-1)
cs=intarr(n) & cs(*)=ist
while total(ss) ne n do begin
t=where(ss eq 0)
mini=min(dm(t,cs(t)),kl)
s=t(kl mod int(n-total(ss)))
ss(s)=1
nss=total(ss)
aa(*,nss-2)=[s,cs(s)]
if nss lt n then begin
t=where(ss eq 0)
xx=where(dm(t,replicate(s,n-nss)) lt dm(t,cs(t)))
sxx=size(xx)
if sxx(0) eq 1 then cs(t(xx))=s
endif
endwhile
return,aa
end
NNG
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NAME:
NNG
Nearest neighbors bestimmen
FUNCTION NNG,dm,ng
sdm=size(dm)
if sdm(0) ne 2 then message,'Distancematrix not 2-dim.'
if sdm(1) ne sdm(2) then message,'Distancematrix not a sqare'
n=sdm(1)
nen=intarr(n)
for i=0,n-1 do begin
mini=min(dm(i,ng(ng(i):ng(i+1)-1)),kl)
nen(i)=ng(ng(i)+kl)
endfor
return,nen
end
PLOT_DNA
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NAME:
plot_dna
Einlesen von DNA Daten von Filen,
Selektieren eines Specimens Spec,
Ausgeben entsprechend TYPE mit einer oder mehreren Moeglichkeiten
aus ['DNA','Ent','cDI','SINE1','SINE4','PB']
oder entsprechend /MULTI, alle Moeglichkeiten in ein Bild
Input File: e.g.
2 1170 2.01071
3 1170 2.07279
4 1170 2.09343
5 1170 2.03847
The all columns must contain numbers, where the first is arbitrary,
the second is the specimen number and the third is the DNA value in
multiples of c.
pro plot_dna,filen,spec,TYPE=dtyp,MULTI=multi
if keyword_set(multi) then begin
if multi eq 1 then !p.multi=[0,3,2,0,0] else !p.multi=[0,multi,2,0,0]
endif else !p.multi=[0,0,0,0,0]
!x.charsize=1.5 & !y.charsize=1.5
d=read_ascii(filen)
sd=size(d)
if sd(0) ne 2 then begin
message,'No data !',/continue
return
endif
if n_params() ge 2 then wh=where(d(1,*) eq spec) $
else wh=lindgen(sd(2))
ds=size(wh)
if ds(0) ne 1 then begin
message,'No data selected !',/continue
return
endif
ih=histogram(d(2,wh),binsize=0.1,min=1.0, max=16.0)
fh=smooth(float(ih),3)
h=fh/float(ds(1))
h(0)=0 ; Damit polyfill nicht Ueberraschungen macht
xx=findgen(151)/10+1.0
if keyword_set(multi) then begin
if multi eq 1 then dtyp=['DNA','Ent','cDI','SINE1','SINE4','PB']
endif
if keyword_set(dtyp) then begin
if typeof(dtyp,/dim) eq 0 then dtyp=[dtyp]
endif else dtyp=['DNA']
st=size(dtyp)
for i=0,st(1)-1 do case dtyp(i) of
'DNA':begin
plot,xx,h,psym=10,yrange=[0.0,15],noclip=0
polyfill,xx,h*100,noclip=0
xyouts,4.0,13,'!5DNA Mean = '+string(total(d(2,wh)/ds(1)), $
format='(f7.2)'),charsize=1
if n_params() gt 1 then $
xyouts,4.0,12,'!5Specimen:'+string(spec,format='(i5)')
end
'Ent':begin
print,'Entropy'
l=h & l(*)=0.0 & l(where(h ne 0.0))=alog10(h(where(h ne 0.0)))
e=-h*l
plot,xx,e,psym=10,yrange=[0.0,0.5],noclip=0
polyfill,xx,e,noclip=0
xyouts,4.0,0.43,'!5Entropy = '+string(total(e),format='(f7.4)'),charsize=1
if n_params() gt 1 then $
xyouts,4.0,0.4,'!5Specimen:'+string(spec,format='(i5)')
end
'cDI':begin
print,'2cDI'
di=h*(xx-2.0)^2
plot,xx,di,psym=10,noclip=0,ytick_get=yv
polyfill,xx,di,noclip=0
syv=size(yv)
yp=yv(syv(1)-1)*0.85
xyouts,4.0,yp,'!52cDI ='+string(alog10(total(di)+1.0)*1.757, $
format='(f7.4)'),charsize=1
if n_params() gt 1 then $
xyouts,4.0,yv(syv(1)-1)*0.8,'!5Specimen:'+string(spec,format='(i5)')
end
'SINE1':begin
z=h*50.*(1.+sin(alog(xx)/alog(2.0)*2.*!pi-!pi*0.5))
plot,xx,z,psym=10,yrange=[0.0,15],noclip=0
polyfill,xx,z,noclip=0
xyouts,4.0,13,'!5SINE1 = '+string(total(z),format='(f7.2)'),charsize=1
if n_params() gt 1 then $
xyouts,4.0,12,'!5Specimen:'+string(spec,format='(i5)')
end
'SINE4':begin
dxx3=3.0*(xx-2.0)/14.>0.
dz3=h*50.*(1.+sin(alog(xx)/alog(2.0)*2.*!pi-!pi*0.5)+dxx3)
plot,xx,dz3,psym=10,yrange=[0.0,15],noclip=0
polyfill,xx,dz3,noclip=0
xyouts,4.0,13,'!5SINE4 ='+string(total(dz3),format='(f7.2)'),charsize=1
if n_params() gt 1 then $
xyouts,4.0,12,'!5Specimen:'+string(spec,format='(i5)')
end
'PB':begin
dbr=xx & dbr(*)=-1.0
dbr(0:7)=0.0 & dbr(8:13)=1.0 & dbr(28:34)=1.0 & dbr(65:75)=1.0
dbr=h*dbr*100.0
plot,xx,dbr,psym=10,yrange=[-15.0,15.0],ystyle=1,noclip=0
polyfill,xx,dbr,noclip=0
xyouts,4.0,11,'!5Ploidy Balance ='+string(total(dbr), $
format='(f7.2)'),charsize=1
if n_params() gt 1 then $
xyouts,4.0,9,'!5Specimen:'+string(spec,format='(i5)')
end
else:
endcase
end
SLIDE_IMAGE
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NAME:
SLIDE_IMAGE
PURPOSE:
Create a scrolling graphics window for examining large images.
By default, 2 draw widgets are used. The left draw widget shows
a reduced version of the complete image, while the draw widget on
the right displays the actual image with scrollbars that allow sliding
the visible window.
CALLING SEQUENCE:
SLIDE_IMAGE [, Image]
INPUTS:
Image: The 2-dimensional image array to be displayed. If this
argument is not specified, no image is displayed. The
FULL_WINDOW and SCROLL_WINDOW keywords can be used to obtain
the window numbers of the 2 draw widgets so they can be drawn
into at a later time.
KEYWORDS:
CONGRID: Normally, the image is processed with the CONGRID
procedure before it is written to the fully visible
window on the left. Specifying CONGIRD=0 will force
the image to be drawn as is.
FULL_WINDOW: A named variable in which to store the IDL window number of \
the non-sliding window. This window number can be used with
the WSET procedure to draw to the scrolling window at a later
point.
GROUP: The widget ID of the widget that calls SLIDE_IMAGE. If this
keyword is specified, the death of the caller results in the
death of SLIDE_IMAGE.
ORDER: This keyword is passed directly to the TV procedure
to control the order in which the images are drawn. Usually,
images are drawn from the bottom up. Set this keyword to a
non-zero value to draw images from the top down.
REGISTER: Set this keyword to create a "Done" button for SLIDE_IMAGE
and register the widgets with the XMANAGER procedure.
The basic widgets used in this procedure do not generate
widget events, so it is not necessary to process events
in an event loop. The default is therefore to simply create
the widgets and return. Hence, when register is not set,
SLIDE_IMAGE can be displayed and the user can still type
commands at the "IDL>" prompt that use the widgets.
RETAIN: This keyword is passed directly to the WIDGET_DRAW
function, and controls the type of backing store
used for the draw windows. If not present, a value of
2 is used to make IDL handle backing store.
SLIDE_WINDOW: A named variable in which to store the IDL window number of
the sliding window. This window number can be used with the
WSET procedure to draw to the scrolling window at a later
time.
TITLE: The title to be used for the SLIDE_IMAGE widget. If this
keyword is not specified, "Slide Image" is used.
TOP_ID: A named variable in which to store the top widget ID of the
SLIDE_IMAGE hierarchy. This ID can be used to kill the
hierarchy as shown below:
SLIDE_IMAGE, TOP_ID=base, ...
.
.
.
WIDGET_CONTROL, /DESTROY, base
XSIZE: The maximum width of the image that can be displayed by
the scrolling window. This keyword should not be confused
with the visible size of the image, controlled by the XVISIBLE
keyword. If XSIZE is not specified, the width of Image is
used. If Image is not specified, 256 is used.
XVISIBLE: The width of the viewport on the scrolling window. If this
keyword is not specified, 256 is used.
YSIZE: The maximum height of the image that can be displayed by
the scrolling window. This keyword should not be confused
with the visible size of the image, controlled by the YVISIBLE
keyword. If YSIZE is not present the height of Image is used.
If Image is not specified, 256 is used.
YVISIBLE: The height of the viewport on the scrolling window. If
this keyword is not present, 256 is used.
OUTPUTS:
None.
COMMON BLOCKS:
None.
SIDE EFFECTS:
Widgets for displaying a very large image are created.
The user typically uses the window manager to destroy
the window, although the TOP_ID keyword can also be used to
obtain the widget ID to use in destroying it via WIDGET_CONTROL.
RESTRICTIONS:
Scrolling windows don't work correctly if backing store is not
provided. They work best with window-system-provided backing store
(RETAIN=1), but are also usable with IDL provided backing store
(RETAIN=2).
Various machines place different restrictions on the size of the
actual image that can be handled.
MODIFICATION HISTORY:
7 August, 1991, Written by AB, RSI.
10 March, 1993, ACY, Change default RETAIN=2
23 Sept., 1994 KDB, Fixed Typo in comments. Fixed error in
Congrid call. xvisible was used instead of yvisible.
SLIDE_IMAGE_TC
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NAME:
SLIDE_IMAGE_TC
PURPOSE:
Create a scrolling graphics window for examining large images.
By default, 2 draw widgets are used. The left draw widget shows
a reduced version of the complete image, while the draw widget on
the right displays the actual image with scrollbars that allow sliding
the visible window.
CALLING SEQUENCE:
SLIDE_IMAGE_TC [, Image]
INPUTS:
Image: The 2-dimensional image array to be displayed. If this
argument is not specified, no image is displayed. The
FULL_WINDOW and SCROLL_WINDOW keywords can be used to obtain
the window numbers of the 2 draw widgets so they can be drawn
into at a later time.
KEYWORDS:
CONGRID: Normally, the image is processed with the CONGRID
procedure before it is written to the fully visible
window on the left. Specifying CONGIRD=0 will force
the image to be drawn as is.
FULL_WINDOW: A named variable in which to store the IDL window number of \
the non-sliding window. This window number can be used with
the WSET procedure to draw to the scrolling window at a later
point.
GROUP: The widget ID of the widget that calls SLIDE_IMAGE. If this
keyword is specified, the death of the caller results in the
death of SLIDE_IMAGE.
ORDER: This keyword is passed directly to the TV procedure
to control the order in which the images are drawn. Usually,
images are drawn from the bottom up. Set this keyword to a
non-zero value to draw images from the top down.
REGISTER: Set this keyword to create a "Done" button for SLIDE_IMAGE
and register the widgets with the XMANAGER procedure.
The basic widgets used in this procedure do not generate
widget events, so it is not necessary to process events
in an event loop. The default is therefore to simply create
the widgets and return. Hence, when register is not set,
SLIDE_IMAGE can be displayed and the user can still type
commands at the "IDL>" prompt that use the widgets.
RETAIN: This keyword is passed directly to the WIDGET_DRAW
function, and controls the type of backing store
used for the draw windows. If not present, a value of
2 is used to make IDL handle backing store.
SLIDE_WINDOW: A named variable in which to store the IDL window number of
the sliding window. This window number can be used with the
WSET procedure to draw to the scrolling window at a later
time.
TITLE: The title to be used for the SLIDE_IMAGE widget. If this
keyword is not specified, "Slide Image" is used.
TOP_ID: A named variable in which to store the top widget ID of the
SLIDE_IMAGE hierarchy. This ID can be used to kill the
hierarchy as shown below:
SLIDE_IMAGE_TC, BASE_ID=base, ...
.
.
.
WIDGET_CONTROL, /DESTROY, base
XSIZE: The maximum width of the image that can be displayed by
the scrolling window. This keyword should not be confused
with the visible size of the image, controlled by the XVISIBLE
keyword. If XSIZE is not specified, the width of Image is
used. If Image is not specified, 256 is used.
XVISIBLE: The width of the viewport on the scrolling window. If this
keyword is not specified, 256 is used.
YSIZE: The maximum height of the image that can be displayed by
the scrolling window. This keyword should not be confused
with the visible size of the image, controlled by the YVISIBLE
keyword. If YSIZE is not present the height of Image is used.
If Image is not specified, 256 is used.
YVISIBLE: The height of the viewport on the scrolling window. If
this keyword is not present, 256 is used.
OUTPUTS:
None.
COMMON BLOCKS:
None.
SIDE EFFECTS:
Widgets for displaying a very large image are created.
The user typically uses the window manager to destroy
the window, although the TOP_ID keyword can also be used to
obtain the widget ID to use in destroying it via WIDGET_CONTROL.
RESTRICTIONS:
Scrolling windows don't work correctly if backing store is not
provided. They work best with window-system-provided backing store
(RETAIN=1), but are also usable with IDL provided backing store
(RETAIN=2).
Various machines place different restrictions on the size of the
actual image that can be handled.
MODIFICATION HISTORY:
7 August, 1991, Written by AB, RSI.
10 March, 1993, ACY, Change default RETAIN=2
STRPARSE
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NAME:
STRPARSE
PURPOSE:
Parses the string LINE using the characters in DELIM as delimiters.
Puts individual pieces into consecutive locations in LIST.
CATEGORY:
String Processing
CALLING SEQUENCE:
Result = STRPARSE( LINE, DELIM [, LIST])
INPUTS:
LINE
Character string.
DELIM
Character string. Each Character of DELIM is used as a delimiter.
OPTIONAL INPUT PARAMETERS:
None.
KEYWORD PARAMETERS:
None.
OUTPUTS:
Returns the number of pieces found minus one i.e. the index of the last
element of LIST if LIST is provided. If LINE is a null string or not a
string, the function returns -1.
OPTIONAL OUTPUT PARAMETERS:
LIST
Character array. If name is provided, the pieces of LINE resulting
from the parsing process are returned in consecutive locations in LIST.
COMMON BLOCKS:
None.
SIDE EFFECTS:
None.
RESTRICTIONS:
None.
PROCEDURE:
Straightforward. Using the function TYPE from MIDL.
MODIFICATION HISTORY:
Created 15-JUL-1991 by Mati Meron.
TRACE
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NAME:
TRACE
PURPOSE: Define a path through an image using the image display
system and the cursor/mouse. This routine is designed to
be used on images which have been displayed with the TVIM
procedure.
CATEGORY: Image processing.
CALLING SEQUENCE:
R = trace(xsize,ysize)
R = trace(xsize,ysize,xverts, yverts, /nodes, /restore, /silent)
INPUTS:
xsize,ysize Size of image array
KEYWORD INPUT PARAMETERS:
RESTORE if set, originaly displayed image is restored to its
original state on completion.
NODES If set index array is not returned.
Use this option when positions x and y vertices are
all that are required.
X0,Y0 Lower left image coordinates, default=0,0
ZOOM Two element vector specifying zoom factor in x and y,
if omitted, [1.,1.] is assumed. A single scalar value
will set both the x and y zoom factors.
SILENT If set no intructional printout is issued at the
beginning of execution
OUTPUTS:
Function result = subscript vector of pixels along defined path.
OPTIONAL OUTPUTS:
XVERTS Vector of x vertices of traced path
YVERTS Vector of y vertices of traced path
COMMON BLOCKS:
None.
SIDE EFFECTS:
Display is changed if RESTORE is not set.
RESTRICTIONS:
Only works for interactive, pixel oriented devices with a
cursor and an exclusive or writing mode.
A path may have at most 1000 vertices. If this is not enough
edit the line setting MAXPNTS.
PROCEDURE:
The exclusive-or drawing mode is used to allow drawing and
erasing objects over the original object.
The operator marks the vertices of the path, either by
dragging the mouse with the left button depressed or by
marking individual points along the path by clicking the
left mouse button, or with a combination of both.
The center button removes the most recently drawn points.
Press the right mouse button when finished. On exit gaps in the
traced path are filled by interpolation
Adapted from DEFROI by : Paul Ricchiazzi oct92
Earth Space Research Group, UCSB
Karsten Rodenacker Jul93 (no !x,!y)
VOL_TIFF_READ
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NAME:
VOL_TIFF_READ
PURPOSE:
Input of 3d-images from sequences of section tif-files and definition of
data array [red, green, blue].
File sequences have to be in the form xxxxxyyy.zzz where xxxxx is an arbitrary
string, yyy a number, starting from NUMBER_FIELD and zzz an arbitrary string
according EXTENSION
CATEGORY:
3d image I/O
CALLING SEQUENCE:
vol = vol_tiff_read(name, NUMBER_FIELD='000', NUMBER_SECTIONS=10)
INPUTS:
name: Name prefix of the file sequence, e.g. 'abcd'
OPTIONAL INPUTS:
none
KEYWORD PARAMETERS:
NAME: Full file sequence specification, no pickfile is used.
e.g. '/mnt/iliad/series/abcd'
SPLITTED: If set the data are returned into variables
given by keywords RED GREEN BLUE and not
merged into one array. Function will return 1.
RED: Variable for red channel
GREEN: Variable for green channel
BLUE: Variable for blue channel
NUMBER_FIELD: A string describing the first section
image to be read in, e.g. '27'. ['000']
NUMBER_SECTIONS:Number of images to be read in starting from NUMBER_FIELD
[all found]
EXTENSION: A string describing the extension ['tif']
CLSM: Variable to contain a clsm privat tiff header
COLOR: Variable which is set to 1 in case of color
images. Resulting volume is dimension either
[3,x,y,z] (color) or [x,y,z] (grey)
VERBOSE: Verbose mode
PROCEDURE:
Reads sequencially tiff images into a buffer
EXAMPLE:
MODIFICATION HISTORY:
Tue Jul 29 08:23:46 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
WD3D
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NAME:
WD3D
PURPOSE:
Display, analysis and count of 3D Daten
CATEGORY:
3D image analysis
CALLING SEQUENCE:
WD3D only after call of d3l_n
OPTIONAL INPUTS:
Labelled image
KEYWORD PARAMETERS:
General
NOGALLERY: No gallery is displayed (def. 0)
XVISIBLE
YVISIBLE: Size of gallery (def. 512,512)
BOX_ALL Start default box size all (32,32,depth)
For automatic signal count
NOSIGNAL_COUNT: No automatic signal count (def. 0)
MIN_SIGNAL_VOLUME: Min. signal volume (voxel) (def. 10)
THRESH_TOPHAT: Threshold TOPHAT (def. 40)
SIZE_TOPHAT: Size of TOPHAT (def. 3)
SIZE_OPENING: Size of opening after tophat (def. 1)
For labelling functions
LABEL: To reserve space for label volumes
NAM_LABEL: Name for label volume file ('')
SIZE_NUCLEUS_OPEN: Size of opening nucleus (def. 2)
MIN_NUCLEUS_VOLUME Minimum nucleus volume (def. 3000)
LONG: integer signal label volume (def. byte)
Misc
GROUP: Widget_id of main widget
REBUILD: Forces rebuild of widgets (for size changes)
COLOR: n/a
VERBOSE: Full messages
Keywords used from d3l_n,
not used from wd3d (see d3l_n) !
OVER_COLOR:
PATH:
NAME:
NOTOPHAT:
NUMBER_FIELD:
EXTENSION:
NUMBER_SECTIONS:
RESULT:
OUTPUTS:
Count informations
Labelled image
OPTIONAL OUTPUTS:
Count informations
Labelled image
COMMON BLOCKS:
WD3D_DAT contains data
WD3D_INT internal data
SIDE EFFECTS:
RESTRICTIONS:
Needs preceeding call of procedure D3L_N,
to load data and establish common's
PROCEDURE:
1 Load data by calling d3l_n or the simple interface main
2 Call wd3d
EXAMPLE:
main,/LAB,PATH='~/series'
MODIFICATION HISTORY:
Fri Jul 25 16:52:54 1997, Karsten Rodenacker
Tue Jul 22 16:28:25 1997, Karsten Rodenacker
Tue Jul 29 08:15:26 1997, Karsten Rodenacker
<iliad@janus.gsf.de>
WD3D_CONTIN
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NAME:
wd3d_contin
pro wd3d_contin,name,PRINT=prin
common wd3d_int
boxarr=strarr(1000)
wd3d_read,name
wd3d_count,tit=name,histogram=hi
print,'Frequencies:',hi(1:7),format='(a,7i4)'
if keyword_set(prin) then begin
set_plot,'ps'
wd3d_count,tit=string(name,hi(1:7),format='(a,x,7i4)')
lprint,/return
endif
end
WD3D_MERGE
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NAME:
wd3d_merge
pro wd3d_merge,wild,onam
na=findfile(wild,cou=cna)
b=strarr(1000)
b(0)=string(wild,cna,onam,format="(a,t60,i3,x,a)")
print,b(0)
k=1
for i=0,cna-1 do begin
print,na(i)
a=read_s_ascii(na(i))
sa=size(a)
l=0
for j=1,sa(1)-1 do if strlen(a(j)) gt 30 then begin
b(k)=string(a(j),i,format="(a,i4)")
k=k+1
endif
endfor
write_s_ascii,onam,b(0:k)
end
WRITE_S_ASCII
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NAME:
write_s_ascii
pro write_s_ascii,name,a
sa=size(a)
if sa(0) ne 1 and sa(2) ne 7 then message, 'Not 1-dim. stringarray !'
openw,lf,name,/get_lun
if !version.arch eq 'vax' then for i=0,sa(1)-1 do writeu,lf,a(i) $
else for i=0,sa(1)-1 do printf,lf,a(i)
free_lun,lf
end