How to run CIP on a Mac 
 

mycomputer:CIPsite$ make

mycomputer:CIPsite$ sudo make install

Install CIP


On your make you need to have a fortran compiler, either gfortran or g77.

To build and install from source:

  1. Unpack the archive
  2. To compile all programs type: make
  3. To install all binaries in /usr/local/bin type: sudo make install

Complete READ-ME file for installation included in software download:  → cip.tar.gz

 

mycomputer$cd CIPsite/sample$

mycomputer:CIPsite:sample$ cip1a
--------------------------------------------------------
*cip1a: azi,err,inca,incp, max,min,maxphas,Tindex
........maximum image size is.......1542288
........re-written for macosx and g77......june-06
........inclinations >90 wrap around.......june-08
........inclinations <90 wrap (corrected)...feb-10
........writes wrap index into fmax file....mar-11
........cirpol background sub corrected.....aug-12
........does 4 tilts........................feb-13
--------------------------------------------------------
***** calling control
name of controle file >

Run CIP1A


← Set the path to the folder containing the sample files.

← cip1a = start of program

The program opens with a welcome text

 

 

y.ctrlA
no.of tilts and tilt type: 4 1
back1,back2,flaresub,camcorr: 1 1 1 1
../../calib/axio-micro-660-700.CAL
../../calib/incA-incP-20-lin-660-700.LUT
--------------------------------------------------------
***** calling readfiles
input/213mn.010
input/213mn.020
input/213mn.030
input/213mn.040
input/213mn.050
input/213mn.060
input/213mn.070
input/213mn.080
input/213mn.090
input/213mn.100
input/213mn.110
input/213mn.120
input/213mn.130
input/213mn.140
input/213mn.150
input/213mn.160
input/213mn.170
input/213mn.180
input/213mn.eup
input/213mn.sup
input/213mn.wup
input/213mn.nup
input/213mn.cirpol
input/213mn.backR
input/213mn.backT
--------------------------------------------------------
***** calling viewpix
viewpix: x,y coordinates (end = (0,0)) >

← Name of control file

Here, the name is y.ctrlA (for CIP1A).

The contents of the control file (mostly file names) is printed on the screen

 

 

0,0
--------------------------------------------------------
***** calling calibrate
--------------------------------------------------------
***** calling viewpix after calibration *****
viewpix: x,y coordinates (end = (0,0)) >

← View single pixel before calibration

Type the X-Y coordinates of the desired pixel

Here, (0,0) is selected - no pixel is viewed.

 

0,0
--------------------------------------------------------
***** calling curfit
--------------------------------------------------------
***** calling convert

inca:

+ 16 *
+ 32 ***
+ 48 *****
+ 64 ********
+ 80 *********
+ 96 *********
+ 112 **********
+ 128 ************
+ 144 **************
+ 160 ********************
+ 176 ***********************************************
+ 192 **************************************************
+ 208
+ 224
+ 240
+ 256

amplitude image incamp
0-1-2-5-95-98-99-100 % = 0 18 28 45 186 189 191 210
input cut-off values (min,max) >

← View single pixel after calibration

Type the X-Y coordinates of the desired pixel

(Need to add 1 to X and Y as read from Image SXM because in CIP, coordinates start with 1 - not 0.)

It may be useful to view the greyvalues of certain pixels (brightest or darkest) after calibration. Knowing these values may help to crop the histogram (see below)

 

A histogram of amplitudes is displayed (256 grey values)

From the amplitudes, the primary inclinations INCA are calculated.

In most cases, the histogram needs cropping: one has to determine the minimum and maximum values that correspond to 0° and 90° inclination, respectively.

The decision is usually based on a percentile cut-off on the histogram.

The numbers show below the histogram are the grey values of the 0, 1, 2, 5, 95, 98, 99 and 100 percentile.

 

 

0,186

incp:

+ 16 ********
+ 32 ************
+ 48 ***************
+ 64 ******************
+ 80 *******************
+ 96 *************************
+ 112 *********************************
+ 128 ************************************
+ 144 *******************************************
+ 160 *************************************************
+ 176 **************************************************
+ 192 *********
+ 208
+ 224
+ 240
+ 256

inclination image from cirpol
0-1-2-5-95-98-99-100 % = 0 7 14 28 174 178 181 230
input cut-off values (min,max) >

← Select cut-offs for amplitude

To crop the histogram of amplitudes between the 0% and 95% percentile, the values 0,186 are selected

 

A histogram of grey values of the cirpol image is displayed (256 grey values)

From these values, the primary inclinations INCP are calculated.

In most cases, the histogram needs cropping: one has to determine the minimum and maximum values that correspond to 0° and 90° inclination, respectively.

The decision can be based on measured grey values (Viewpix) or on a percentile cut-off on the histogram.

The numbers show below the histogram are the grey values of the 0, 1, 2, 5, 95, 98, 99 and 100 percentile.

 

0,174
--------------------------------------------------------
***** calling writeprimary
--------------------------------------------------------
***** calling writefiles
--------------------------------------------------------
***** calling polefigure
-> maximum of polefigure is at (25, 5): 6.26243
--------------------------------------------------------
***** calling ava
polamp=2 => cirpol used for coi
name of clut:
../../clut/CIP-P-standard.CLUT

← Select cut-offs for cirpol

To crop the histogram of cirpol grey values between the 0% and 95% percentile, the values 0,174 are selected

 

The program ends by typing the maximum of the pole figure - here it is 6.26 (times uniform density). Note, however, that this pole figure only covers one half of the orientation half space.

 

CIP-P-standard.CLUT is used to color code the c-axis orientation image (COI1A)

 

mycomputer:CIPsite:sample$ cip1b
--------------------------------------------------
*cip1b: azi/inc from azi/inc/tindex
no polefigure !
maximum image size is 1542288
re-written for macosx and g77 june-06
last update march-07
--------------------------------------------------
***** calling control
name of controle file >

Run CIP1B


← cip1b = start the program

The program opens with a welcome text

 

 

y.ctrlB
../../calib/axio-micro-660-700.CAL
../../calib/incA-incP-20-lin-660-700.LUT
--------------------------------------------------
***** calling readfiles
CIP1A/213mn.AZI
CIP1A/213mn.INCP
CIP1A/213mn.Tindex
--------------------------------------------------
***** calling convert2
***** calling writefiles
--------------------------------------------------
***** calling ava
../../clut/CIP-P-standard.CLUT

← Name of control file

Here, the name is y.ctrlB (for CIP1B).

 

The input file names are printed on the screen
AZI = azimuth
INCP = primary inclination file from cirpol (0° - 90°)
Tindex = tilt index file used derived full inclination (0° - 180°)

 

CIP-P-standard.CLUT is used to color code the c-axis orientation image (COI1B)

 

 

mycomputer:CIPsite:sample$ cip2
----------------------------------------------------
cip2: coi/mis/edg from azi/inc/mask
maximum image size is 6000000
re-written for macosx and g77 apr-04
>>> reads square (CLUT) and stereo (POL)
edg2s sum of difference with 2 neighbours (0-180)
edg4a 2*av of difference with 4 neighbours (0-180)
last update (polfig correction) march-07
last update (edges) august-07
+MASK considers mask in misor and edge june-08
----------------------------------------------------
*calling control
name of controle file :

Run CIP2


← cip2 = start the program

The program opens with a welcome text

 

 

y.ctrl2
----------------------------------------------------
*calling readfiles
*calling readfiles: azi
CIP1A/213mn.azi
*calling readfiles: inc
CIP1B/213mn.inc
*calling readfiles: mask
input/213mn.mask
* xdim*ydim=itot 1300 1000 1300000
----------------------------------------------------
*calling segment
----------------------------------------------------
*calling writefiles
CIP2/213mn.EDG2s
CIP2/213mn.EDG4a
CIP2/213mn.MISN2
CIP2/213mn.MISE2
CIP2/213mn.MISH2
CIP2/213mn.MIS-45-90
-------------------------------------------------
*calling polefigure using mask
* imask = 1 (0=no,1=yes)
* polcorr = 1 (option 1-5)
--> maximum of polefigure is at (25, 5): 5.79747
-------------------------------------------------
*calling ava
../../clut/CIP-P-spectrum.CLUT
-------------------------------------------------
mycomputer:CIPsite:sample$

← Name of control file

Here, the name is y.ctrl2 (for CIP2).

 

The input file names are printed on the screen:

AZI, INC, mask

 

The result file names are printed on the screen:

EDG2s, EDG4a = orientation gradient images

MISN2, MISE2, MISH2 and MIS-45-90 = misorientation images

 

The maximum pole figure density is indicated

Here, it is 5.78

Please note this number or keep a log of the dialogue with the program.

 

CIP-P-spectrum.CLUT is used to color code the c-axis orientation image (COI2)

 

 

mycomputer:CIPsite:sample$ cip4
----------------------------------------------------
*cip4: coi/mis/edg from azi/inc/mask (=cip2)
4 reference directions (*.ctrl4)
maximum image size is 6000000
maximum image width is 3000
re-written for macosx and g77 mar-04
>>> reads square (CLUT) and stereo (POL)
edg8a 2*av of difference with 8 neighbours (0-180)
edg8m max of difference with 8 neighbours
last update (polefig corr) march-07
last update (edges) august-07
+MASK considers mask in misor and edge june-08
----------------------------------------------------
*calling control
name of controle file >

Run CIP4


← cip4 = start the program

The program opens with a welcome text

 

 

y.ctrl4
----------------------------------------------------
*calling readfiles
*calling readfiles: azi
CIP1A/213mn.AZI
*calling readfiles: inc
CIP1B/213mn.INC
*calling readfiles: mask
input/213mn.mask
* xdim*ydim=itot 1300 1000 1300000
----------------------------------------------------
*calling segment
----------------------------------------------------
*calling writefiles
CIP4/213mn.EDG8a
CIP4/213mn.EDG8m
CIP4/213mn.MISr1_045_052
CIP4/213mn.MISr2_135_052
CIP4/213mn.MISr3_045_128
CIP4/213mn.MISr4_135_128
-------------------------------------------------
*calling polefigure using mask
* imask = 0 (0=no,1=yes)
* polcorr = 1 (option 1-5)
--> maximum of polefigure is at (25, 5): 5.17814
-------------------------------------------------
*calling ava
../../clut/qtz20-pale.POL
-------------------------------------------------
mycomputer:CIPsite:sample$

← Name of control file

Here, the name is y.ctrl4 (for CIP4).

 

The input file names are printed on the screen:

AZI, INC, mask

 

The result file names are printed on the screen:

EDG8a, EDG8m = orientation gradient images

MISr1_045_052, MISr2_135_052, MISr3_045_128, MISr4_135_128 =

4 misorientation images w/r to 4 octahedral planes

 

imask= 0, i.e., no mask is used.

The maximum pole figure density is indicated

Here, it is 5.178

Please note this number or keep a log of the dialogue with the program.

 

qtz20-pale.CLUT is used to color code the c-axis orientation image (COI4).

This achieves an impression of viewing the thin section under crossed polarizer with the waveplate inserted.