# Last edited on 2018-06-25 21:02:41 by stolfilocal
# Processing images captured by the UFF microscope

RENAMING FILES

  Fetched scans made by Gustavo around 2017-06 from his Google drive
    
    https://drive.google.com/drive/folders/0B4RFBC26-_NnbDVvc1c2Q0dzajg
    
  Also downloaded the scane made with the v2.0 in 2018-06:
  
    https://drive.google.com/drive/folders/1hWlXxL7WprhLK7vBAj09TWOdlJ2XBMp2
  
  Downloaded and unzipped in directory "new". Renamed all files as
  described below.
  
STOLFI'S NAMING SCHEME

  The data obtined in one capture session (/scanset/) consists of a set
  of images of the same object taken in one run, with different
  illuminations, different focus midplanes (by variable zoom or by
  moving the camera), and possibly from different viewing directions
  (by tilting the object and/or tilting and/or displacing the camera).

  In each directory there may be a file "00-README"..

  OBJECT DIRECTORIES
  
  All the scansets of a given object are in an /object directory/
  "objs/{OBJNAME}_{NO}", e.g. "objs/flower_01", where
  
    {OBJECT} is a 6-letter descriptive name of the object.

    {NO} is two digits distinguishing similar objects.

  SCANSET DIRECTORIES

  All the files related to each scanset (the captured images and any
  images or files derived from them) are in a /scanset diretory/
  named
  
    {OBJDIR}/{YYYY-MM-DD-HHMM}

  E. g. "objs/flower_01/2017-06-02-0745", where 

    {YYYY-MM-DD-HHMM} is the nominal date and approximate time 
    that the scan was acquired (e.g. of the first image).

  SCASNSET STRUCTURE
  
  The images in the same scanset consist of one or more
  /image stacks/, where all images in each stach are taken
  with the same lighting conditions and viewing direction.
  Each stack is in a /stack directory/

    {SCANSET_DIR}/L_{NL}/V_{NV}/

  E. g. "objs/flower_01/2017-06-02-0745/L_00/V_00/", where 

    {NL} is two digit identifying the lighting conditions,
    usually the position of the primary light source,
    from "00".

    {NV} is two digits identifying the viewing direction. 

  IMAGE STACK STRUCTURE
  
  Within each image stack directory, there may be subdirectories:

    "raw" - captured images for one object, session, 
    light source, and view. Also some processing of
    those images prior to alignment.  It contains

    "align" - aligned images obtained with the {hugin}
    alignment tool (see script {align_images_hugin.sh).

    "clip_{NC}" - detail images clipped from the 
    "align" images, where {NC} is a two-diigt code
    distinguishing the region clipped.

  Within each of these directories, there may be files

       "frame_{FFFFF}.jpg" - the raw captured image.
       The sequence number {FFFFF} (five digits,
       from 00000) is the position of the image 
       in the stack, usually from bottom up.

       "merge.jpg" - the output of {combine} 
       applied to the raw unaligned images.

       "work" - subdirectory with various 
       temporary files.

  RENAMING FILES
  
  See the following scripts:
    
    new/rename_2017-06-10_dirs.sh
    new/rename_2017-06-10_files.sh
    
    new/rename_2018-06-25_dirs.sh
    new/rename_2018-06-25_files.sh

  DISCARDING BAD SETS
  
  The following scans were discarded due to bad exposure 
  or other fatal flaws:
  
    rm -rf objs/sphere_01/2017-06-07-1436
    rm -rf objs/sphere_01/2017-06-07-1510

RUNNING THE ALIGNMENT TOOL

  Running the {hugin} alignment tool on the raw images:
  
    for sub in raw align ; do 
      find objs/ -type d -name "${sub}" -print | sed -e 's:^[.]/::g' -e 's:/'"${sub}"'::g' | sort > .${sub}s
      uniq -d .${sub}s
    done
    bool 1-2 .raws .aligns > .to-align
    
  Excluded manually these trivial directories:

    objs/wpaper_01/2017-05-26-0823/L_00/V_00
    objs/wpaper_01/2017-05-26-0823/L_01/V_00
    objs/wpaper_01/2017-05-26-0823/L_02/V_00
    objs/wpaper_01/2017-05-26-0823/L_03/V_00
    objs/wpaper_01/2017-05-26-0823/L_04/V_00
    objs/wpaper_01/2017-05-26-0823/L_05/V_00

  Aligning the stacks:

    for dir in `cat .to-align` ; do 
      echo "=== ${dir} ==============================="
      align_stack_hugin.sh ${dir} raw
    done

  Re-aligning the some directories:
    
    for led in 0 1 2 3 4 5 ; do 
      dir="objs/flower_01/2017-06-02-0745/L_0${led}/V_00"
      align_stack_hugin.sh ${dir} raw
    done

  Enhancing the contrast of white paper images:
    
    for led in 0 1 2 3 4 5 ; do 
      dir="objs/wpaper_01/2017-05-26-0823/L_0${led}/V_00"
      equalize_raw_images.sh ${dir}
    done

  Re-aligning the white paper images:
    
    for led in 0 1 2 3 4 5 ; do 
      dir="objs/wpaper_01/2017-05-26-0823/L_0${led}/V_00"
      align_stack_hugin.sh ${dir} raweq
    done
        
  Dir not work.

  Converting .tif to .png :
  
    for scs in `cat .convs` ; do 
      echo "=== ${scs} ===================================="
      for file in `cd ${scs} && ls L_*/V_00/align/*.tif` ; do
        convert ${scs}/${file} -alpha Off ${scs}/${file%.*}.png
      done
      ( cd ${scs} && ls -l L_*/V_00/align/*.png )
    done

  Archiving the scansets:

    for scs in `cat .tars` ; do 
      tar -cvzf ${scs}.tgz ${scs}/L_*/V_00/align/frame_*.png
    done

CLIPPING DETAILS FOR PAPER

  Clipping some samples for the paper:
  
    clip_samples.sh objs/flower_01/2017-06-02-0745/L_05/V_00 '320x121+310+480' '50%' 30