tomorecons serie
New box based on v.Fernandez matlab scripts.
Box can take as input :
- scanID
- TomoReconsSeries info
If the previous box is ftseries then the TomoReconsSeries info can be bring with it. Otherwise we will develop a TomoReconsSeries info GUI to let the user enter it. Then this will write a .info files with the needed parameters.
The TomoReconsSeries box should have a pre-processing to check if the scans are from a serie or not. If this is the case then the box should check that the reconstruction is made using the same information. If not the user can:
- ignore it
- reconstruct using the previous reconstruction parameter
- reconstruct previous serie's scans with the new informations
For this process the needed parameters are :
- preset
- reconstruction
- general filter
- rec-overwrite
scripts files are available in /users/tafforea/matlab/tomo_rec_series_dev.m
Then a post-processing box dealing with serie reconstruction will also be developed later.
This is the output of the current tomo_rec_series interface (launched using tomo_rec_series command in matlab)
Do you want all the questions (expert) or just the basic ones (basic)?: : [basic] e
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Information for reconstruction:
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Do you want to use a preset for ring correction? (eg: HR (<2 microns), MR (>2 microns),none) : [MR]
Do you want normal or paganin reconstruction (or both)? : [pag]
Is there a suffix in the folder names of your scans resulting from a pre-reconstruction process (such as optical distortion correction). (none/enter string of suffix) : [none]
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Information for change of data format:
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output format (tif, jp2, vol, raw, none) : [tif]
Compression mode (none, lzw, deflate, etc.) : [none]
output data types in bits (8 or 16) : [16]
Is there at least a vertical series in the group of scans ('no',all individual scans, 'yes', at least 1 vertical series) : [no]
For the 16 bits conversion:
Do you want to use the same 32bits min and max threshold values (yes/no) : [yes]
Do you want all the volume to have same X and Y dimensions (yes/no) : [yes]
The first ring correction presset remove a few rings during the reconstruction
Do you want an addional ring correction on the reconstructed slices (yes/no) : [yes]
Do you want automatic determination of ring correction parameters or do you want to enter them manually (auto/manual) : [auto]
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Extra processing:
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Do you want to invert the contrast of the output data (yes/no) : [no]
Do you want to use autocrop to crop the resulting 16 bits image close to the sample and remove background (yes/no) : [no]
Do you want to automatically rotate your sample to align it within the reconstructed canvas (yes/no) : [no]
Do you want a binning copy of the 16 bits reconstructed volume (yes/no) : [no]
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Overwritting of Previous Processes:
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During the tomographic reconstruction (to 32 bits volfloat), if the program encounter some files from previous processes, should these files be overwritten (yes/no)? : [no]
During the 16 bits reconstruction process, if the program encounter some files from previous processes, should these files be overwritten (yes/no)? : [no]
Creating info file:
/data/visitor/es580/id17/CONCAT__.info
reading tomo_params_info file
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REQUESTED PROCESS SUMMARY:
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- 14 scans will be reconstruced in pag
- A preset (MR) will be applied for pre-reconstruction ring correction
- The 32 bits data will be converted in uint16 tif
- All the scans will have the same min and max threshold values for 16 bits conversions
- All the scans will have the X and Y dimensions for 16 bits conversions
- A ring correction will be applied on the 16 bits data
Ring width (median_size): 50; Security threshold (structure_removal_level): 0.030; Ring arc length (blur_angle): 120
Do you want to start the process? (yes/no) : [yes] n
Edited by payno