Changes for page IDL cheat sheet

Last modified by fwilde on 2025/03/28 19:55

From 21.1 to 22.1 From 54.1 to 55.1

From version 22.1

edited by fwilde
on 2018/11/28 17:53

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To version 54.1

edited by fwilde
on 2024/06/13 13:58

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@@ -1,11 +1,13 @@
--This is an overview of the most commonly used commands during a beamtime.
++== {{id name="IDLcheatsheet-eCoordinatesystem"/}}eCoordinate system ==
--== {{id name="IDLcheatsheet-Coordinatesystem"/}}Coordinate system ==
++Right-handed coordinate system with y-direction along the x-ray beam.
--[[image:attach:P5I.Instrumentation.P05 experimental hutch 2.Micro Tomography setup overview.WebHome@eh2_setup_povray_labeled.png||height="400"]]
++[[image:attach:p05_uct.png||width="700"]]
  == {{id name="IDLcheatsheet-Samplepositioning"/}}Sample positioning ==
++=== {{id name="IDLcheatsheet-Relativemovement"/}}Relative movement ===
++
  (% class="wrapped fixed-table" %)
  |=(((
  IDL command
@@ -15,7 +15,7 @@
  motion
  )))
  |(((
--s_stage_x/z, 1
++##**s_stage_x/z, 1**##
  )))|(((
  move rotation stage in x/z-direction by 1 mm
  )))|(((
@@ -22,14 +22,14 @@
  relative [ mm ]
  )))
  |(((
--s_pos_z, 1
++##**s_pos_x/y/z, 1**##
  )))|(((
--move sample stage in z-direction by 1 mm,
++move sample stage in x/y/z-direction by 1 mm (caution with directions: stage mount on rotation axis)
  )))|(((
  relative [ mm ]
  )))
  |(((
--s_pos_lateral, 1
++##**s_pos, 1**##
  )))|(((
  move sample stage in x-direction by 1 mm, regardless of position of rotation axis
  )))|(((
@@ -36,35 +36,16 @@
  relative [ mm ]
  )))
  |(((
--s_angle, 90
++##**s_angle, 90**##
  )))|(((
  rotate sample around z axis
  )))|(((
  relative [ deg ]
  )))
--|(((
--s_in
--)))|(((
--move sample to "in" position
--)))|(((
--predefined
--)))
--|(((
--s_out
--)))|(((
--move sample to "out" position
--)))|(((
--predefined
--)))
--|(((
--s_change
--)))|(((
--move sample to "change" position
--)))|(((
--predefined
--)))
--(% class="relative-table wrapped" style="width: 72.9307%;" %)
++=== {{id name="IDLcheatsheet-Absolutemovement"/}}Absolute movement ===
++
++(% class="relative-table wrapped" style="width: 67.0892%;" %)
  |=(((
  IDL command
  )))|=(((
@@ -73,7 +73,7 @@
  motion
  )))
  |(((
--goto_s_stage_x/z, 1
++##**goto_s_stage_x/z, 1**##
  )))|(((
  move rotation stage in x/z-direction to 1 mm
  )))|(((
@@ -80,7 +80,7 @@
  absolute [ mm ]
  )))
  |(((
--goto_s_pos_x/y/z, 1
++##**goto_s_pos_x/y/z, 1**##
  )))|(((
  move sample stage in x/y/z-direction to 1  mm
  )))|(((
@@ -87,14 +87,16 @@
  absolute [ mm ]
  )))
  |(((
--goto_s_angle, 90
++##**goto_s_angle, 90**##
  )))|(((
--rotate sample around z axis to 90°
++rotate sample around z axis to 90° (**alias command: s_rot**)
  )))|(((
  absolute [ deg ]
  )))
--(% class="relative-table wrapped" style="width: 67.1421%;" %)
++=== {{id name="IDLcheatsheet-Getcurrentposition"/}}Get current position ===
++
++(% class="relative-table wrapped" style="width: 54.0627%;" %)
  |=(((
  IDL command
  )))|=(((
@@ -101,21 +101,76 @@
  description
  )))
  |(((
--pos_s_stage_x/z()
++##**pos_s_stage_x/z()**##
  )))|(((
  return current rotation stage in x/z position
  )))
  |(((
--pos_s_pos_x/y/z()
++##**pos_s_pos_x/y/z()**##
  )))|(((
  return current sample stage in x/y/z position
  )))
  |(((
--pos_s_angle()
++##**pos_s_angle()**##
  )))|(((
  return current rotation stage angle
  )))
++=== {{id name="IDLcheatsheet-Predefinedpositions"/}}Predefined positions ===
++
++(% class="relative-table wrapped" style="width: 55.721%;" %)
++|=(((
++IDL command
++)))|=(((
++description
++)))
++|(((
++##**s_in**##
++)))|(((
++move sample to "in" position
++)))
++|(((
++##**s_out**##
++)))|(((
++move sample to "out" position
++)))
++|(((
++##**s_change**##
++)))|(((
++move sample to "change" position
++)))
++|(((
++##**set_s_in_pos(, 0)**##
++)))|(((
++set s_in position to current stage position, or optionally to e.g. 0.0 mm
++)))
++|(((
++##**set_s_out_dist, 10**##
++)))|(((
++set s_out distance to 10.0 mm
++)))
++
++=== {{id name="IDLcheatsheet-Magnificationsets"/}}Magnification sets ===
++
++(% class="wrapped" %)
++|=(((
++IDL command
++)))|=(((
++description
++)))
++|(((
++##**save_magn_set(, name_add)
++**##
++)))|(((
++save current magnification set, optionally add something to the automatically generated name
++)))
++|(((
++##**restore_magn_set(, name)
++**##
++)))|(((
++restore last magnification set, or optionally load a file with a specific name
++)))
++
  == {{id name="IDLcheatsheet-Detectorpositioning"/}}Detector positioning ==
  (% class="wrapped fixed-table" %)
@@ -127,30 +127,30 @@
  motion
  )))
  |(((
--pressure_on
++##**o_ccd_dist, 5**##
  )))|(((
--enable detector y movement
++move detector in y direction relative by 5 mm
  )))|(((
--\\
++relative [ mm ]
  )))
  |(((
--o_ccd_dist, 5
++##**goto_o_ccd_dist, 30**##
  )))|(((
--move detector in y direction
++move detector in y direction absoilute to 30 mm
  )))|(((
--relative [ mm ]
++\\
  )))
  |(((
--pressure_off
++##**pos_o_ccd_dist()**##
  )))|(((
--disable detector movement
++return current of the camera stage distance
  )))|(((
  \\
  )))
--== {{id name="IDLcheatsheet-Makeimage"/}}Make image ==
++== {{id name="IDLcheatsheet-Slitpositioning"/}}Slit positioning ==
--(% class="wrapped fixed-table" %)
++(% class="wrapped" %)
  |=(((
  IDL command
  )))|=(((
@@ -157,35 +157,130 @@
  description
  )))
  |(((
--i=quick(100) & tv_quick, i & draw_box, [ x1, x2 ,z1 ,z2 ]
++##**slit_oh, rx=1 (rz=1)**##
  )))|(((
--make an image & show image & draw box
++moves oh slit aperture horizontally (vertically) by 1mm
  )))
  |(((
--a=quick_abs(100) & tv_quick, a & draw_box, [ x1, x2 ,z1 ,z2 ]
++##**slit_oh, rdx=1 (rdz=1)**##
  )))|(((
--make an absorption image & show image & draw box
++opens oh the slit aperture horizontally (vertically) by 1 mm
  )))
++|(((
++##**slit_eh2, rx=1 (rz=1)**##
++)))|(((
++moves eh2 slit aperture horizontally (vertically) by 1 mm
++)))
++|(((
++##**slit_eh2, rdx=1 (rdz=1)**##
++)))|(((
++opens eh2 the slit aperture horizontally (vertically) by 1 mm
++)))
++|(((
++##**slit_info**##
++)))|(((
++show all slit positions
++)))
--== {{id name="IDLcheatsheet-Monochromatorpositioning"/}}Monochromator positioning ==
++rx, rdx, rz and rdz can be concatenated in one command (e.g. slit_oh, rx=1, rz=-2, rdx=0.5, rdz=0.5)
++== {{id name="IDLcheatsheet-Makeandsaveimages"/}}Make and save images ==
++
  (% class="wrapped fixed-table" %)
  |=(((
  IDL command
  )))|=(((
  description
++)))
++|(((
++##**i=quick(100) & display_image, BYSTCL(i, 0, 4096)
++**##
++)))|(((
++make an image & scale image (eg. from 0 to 4096, usually from 0 to maximum value the camera can do)
++)))
++|(((
++##**a=quick_abs(100) & display_image, BYTSCL(a, 0, 2)**##
++)))|(((
++make an absorption image & scale image (usually from 0 to to 2)
++)))
++|(((
++##**write_tiff, '/gpfs/current/raw/test_projection.tif', i, /SHORT**##
++)))|(((
++save i as 16-bit integer tiff in /gpfs/...
++)))
++|(((
++##**write_tiff, '/gpfs/current/raw/test_absorption.tif', a, /FLOAT**##
++)))|(((
++save a as 32-bit float tiff in /gpfs/...
++)))
++
++== {{id name="IDLcheatsheet-Macrosmotion+images"/}}Macros motion  + images ==
++
++These macros make images with predefined and internally saved values (like exposure time or display scale). Some move an axis first and then make an image (again with internally saved options likeexposure time, and image type). Use these macros to quickly align you samples.
++
++(% class="relative-table" style="width: 109.112%;" %)
++|=(((
++IDL command
  )))|=(((
--motion
++description
  )))
  |(((
--calc_dcm_energy, 10000, /set
++**{{code language="none"}}qt (, t=100, scale=[0,4096]){{/code}}**
  )))|(((
--set DCM and undulator to 10 keV
++quick transmission image at the current position, optionally set a new exposure time
++)))
++|(((
++**{{code language="none"}}qa (, t=100, scale=[0,2], /ref){{/code}}**
  )))|(((
++quick absorption image at the current position, optionally set new exposure time or force to make a new reference image
++)))
++|(((
++**{{code language="none"}}qp (, t=100, scale=[0,2], /ref){{/code}}**
++)))|(((
++quick phase retreived image at the current position, optionally set new exposure time or for to make a new reference image
++)))
++|(((
++**{{code language="none"}}side, 90 (, t=100, /ref, /rel, imgtype='a') {{/code}}**
++)))|(((
++move rotation state to absolute angle in degrees (unless /rel is set) and make an imge. Image type can optionally be defined as "a'  (absorption), 't' (transmission) or 'p' (phase). Exposure time is also otional
++)))
++|(((
++**{{code language="none"}}sshift, 2 (, t=100, /ref, imgtype='a'){{/code}}**
++)))|(((
++move sample stage laterally relative to current position and make an image at the new position. Optionally set exposure time, make flat field, or set image type)
++)))
++|(((
++##**sz, 2 (, t=100, /ref, imgtype='a')**##
++)))|(((
++move rotation stage up or down relative to current position and make an image at the new position. Optionally set exposure time, make reference image or set the image type.
++)))
++|(((
++**{{code language="none"}}zx, 2 (, t=100, /ref, imgtype='a'){{/code}}
++**
++)))|(((
++move rotation stage left or right relative to current position and make an image at the new position. Optionally set exposure time, make reference image or set the image type.
++)))
++
  \\
++
++{{info title="Monochromator positioning"}}
++ATTENTION: Setting up a Monochromator as well as positioning front end slits is **only** done by the beamline staff!
++
++The commands above may be used by users to realign the beam should it beam profile drift with time.
++{{/info}}
++
++== {{id name="IDLcheatsheet-DCMpositioning"/}}DCM positioning ==
++
++(% class="wrapped fixed-table" %)
++|=(((
++IDL command
++)))|=(((
++description
++)))|=(((
++motion
  )))
  |(((
--dcm_pitch, 0.00001
++##**dcm_pitch, 0.00001**##
  )))|(((
  move 2nd crystal pitch by 0.00001 deg
  )))|(((
@@ -192,7 +192,7 @@
  relative [ deg ]
  )))
  |(((
--goto_dcm_pitch,  -0.03976
++##**goto_dcm_pitch,  -0.03976**##
  )))|(((
  move 2nd crystal pitch to -0.03976 deg
  )))|(((
@@ -199,7 +199,7 @@
  absolute [ deg ]
  )))
  |(((
--reflex_opt
++##**reflex_opt_single**##
  )))|(((
  move 2nd crystal pitch to optimal flux position
  )))|(((
@@ -206,16 +206,159 @@
  \\
  )))
--== {{id name="IDLcheatsheet-Saveanimageastiff"/}}Save an image as tiff ==
++== {{id name="IDLcheatsheet-DMMpositioning"/}}DMM positioning ==
++(% class="fixed-table wrapped" %)
++|=(((
++IDL command
++)))|=(((
++description
++)))|=(((
++motion
++)))
++|(((
++##**dmm_x2_rot, 0.001**##
++)))|(((
++move 2nd crystal pitch by 0.00001 deg
++)))|(((
++relative [ deg ]
++)))
++|(((
++##**goto_dmm_x2_rot,  0.8923
++**##
++)))|(((
++move 2nd crystal pitch to 0.8923 deg
++)))|(((
++absolute [ deg ]
++)))
++
++\\
++
++== {{id name="IDLcheatsheet-Generalsyntax"/}}General syntax ==
++
++(% class="wrapped relative-table" style="width: 45.5603%;" %)
++|=(((
++Functionality
++)))|=(((
++IDL syntax
++)))
++|(((
++chaining commands
++)))|(((
++command_1 **&** command_2 **&** ...
++)))
++|(((
++absolute movement
++)))|(((
++**goto_**//motor//, position
++)))
++|(((
++relative movement
++)))|(((
++//motor//, position
++)))
++|(((
++current motor position
++)))|(((
++**pos_**//motor//()
++)))
++
++== {{id name="IDLcheatsheet-BeamshutterandInterlockcontrol"/}}Beamshutter and Interlock control ==
++
++(% class="wrapped relative-table" style="width: 75.0455%;" %)
++|=(((
++IDL command
++)))|=(((
++description
++)))
++|(((
++##**bs_info**##
++)))|(((
++prints an overview of the beamline beamshutter status
++)))
++|(((
++##**bsoh_open / bsoh_close**##
++)))|(((
++opens / closes the optics hutch beamshutter. Closing the OH beamshutter will close all following beamshutters (EH1, EH2)
++)))
++|(((
++##**bseh1_open / bseh1_close**##
++)))|(((
++opens / closes the EH1 beamshutter. Opening will open the OH beamshutter as well. Closing the OH beamshutter will the EH2 beamshutter as well
++)))
++|(((
++##**bseh2_open / bseh2_close**##
++)))|(((
++opens / closes the EH2 beamshutter. Openening will open the OH and EH1 beamshutters as well.
++)))
++|(((
++##**ics_info**##
++)))|(((
++prints an overview of the beamline interlock status
++)))
++|(((
++##**oh_break_ics**##
++)))|(((
++closes all P05 beamshutters and breaks OH door interlock. P06 beamshutter must be closed for this command to work!
++)))
++|(((
++##**eh1_break_ics**##
++)))|(((
++closes EH1 beamshutter (and EH2 beamshutter  if open) and breaks EH1 door interlock
++)))
++|(((
++##**eh2_break_ics**##
++)))|(((
++closes EH2 beshutter and breaks EH2 door interlock
++)))
++
++== {{id name="IDLcheatsheet-Helpermacros"/}}Helper macros ==
++
++The helper macros may help to align a sample quickly. Mainly, these are motion commands which subsequently make an image with predefined values.
++
  (% class="wrapped" %)
  |=(((
  IDL command
  )))|=(((
--desciption
++description
  )))
  |(((
--write_tiff, '/gpfs/current/raw/test.tif', i, /SHORT
++helper_object, /info
  )))|(((
--save i as 16-bit tiff in /gofs/...
++show predefined values
  )))
++|(((
++\\
++)))|(((
++\\
++)))
++|(((
++\\
++)))|(((
++\\
++)))
++|(((
++\\
++)))|(((
++\\
++)))
++|(((
++\\
++)))|(((
++\\
++)))
++|(((
++\\
++)))|(((
++\\
++)))
++|(((
++\\
++)))|(((
++\\
++)))
++|(((
++\\
++)))|(((
++\\
++)))

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@@ -1,1 +1,1 @@
--109167004
++365835076

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@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/P5I/pages/109167004/IDL cheat sheet
++https://confluence.desy.de/spaces/P5I/pages/365835076/IDL cheat sheet

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