#   PURPOSE:
#   Basic tools: microscopy simulations, file conversion.
#
#   FILE USAGE:
#   Save the file with a name of your choice and the .tcl extension. Then
#   'source' it in Huygens. The below procedures can be called from the
#   Huygens Tcl Scripting shell.
#
#
#
#   Authors:
#   Dr. Jose Vina,
#   Daniel Sevilla.
#
#   Copyright: 
#   Scientific Volume Imaging Holding BV
#   Marathon 9E,
#   1213 VB Hilversum,
#   The Netherlands,
#  
# 



# Convert the file type of all the files in a folder.
#
# USAGE example: fileConverter "/home" "/tmp" tiff hdf5
#
proc fileConverter { srcDir destDir inType outType } {

    # Retrieve the list of files stored in the source directory.
    set imgList [glob "${srcDir}*"]
    
    # Proceed to open the images and save them with a different extension.
    foreach image $imgList {
        
        # Check whether the image has the extension we are looking for.
        if { [string match "*.$inType" $image] } {
            
            # First open the image.
            set originalImg [img open $image]
            
            # Save the image with a different extension.
            $originalImg save "${destDir}$originalImg" -type $outType
            
            # Close the image to free memory.
            $originalImg del
        }
    }
}




# Adds photon noise up to a given SNR value to an image opened in Huygens.
#
# USAGE example: addNoise image 25
#
proc addNoise { image snr } {   

    # First check if the SNR value is sensible.
    if {$snr > 100 } {set snr 100}
    if {$snr < 3   } {set snr 3}

    # Find the image maximum intensity across all channels.
    set rangeList [$image range]
    set max 0
    foreach {maxTag maxValue minTag minValue} $rangeList {
        if {$maxValue > $max} {
            set max $maxValue
        }
    }

    # Calculate how much noise should be added.
    set ppu [expr {$snr * $snr / $max}]

    # Add noise.
    $image pnoise -> $image -ppu $ppu
}

# Simulates microscopy acquisition creating a synthetic bead and a PSF.
#
# USAGE example: simulateImageAcquisition 0.5 dest widefield 40
#
proc simulateImageAcquisition {beadSize result {mType "confocal"} {snr 100}} {

    # Create empty images.
    set beadImg [img create "beadImg" -type float -dim {32 32 32 0}]
    set fftBead [img create "fftBead" -type float -dim {32 32 32 0}]
    set theoPsf [img create "theoPsf" -type float -dim {32 32 32 0}]
    set fftPsf  [img create "psfFFT"  -type float -dim {32 32 32 0}]

    # Create a synthetic bead.
    $beadImg gensphere -> $beadImg -r $beadSize

    # Show the synthetic bead.
    $beadImg show

    # Set the microscope type, which plays a role in the acquisition result. 
    $beadImg setp -micr $mType

    # Calculate the FFT of the bead image.
    $beadImg fft -> $fftBead -dir f

    # Generate a theoretical PSF for the microscopic settings of the bead.
    $beadImg genpsf -> $theoPsf -dims parent

    # Calculate the FFT of the theoretical PSF.
    $theoPsf fft -> $fftPsf -dir f 

    # Multiply the two FFT's as in the Convolution Theorem.
    $fftBead * $fftPsf -> $result
    
    # Calculate the FFT of the resulting image to go back to real space.
    $result fft -> $result -dir i

    # Set the Fourier domain to 'optical representation'.
    $result optrep -> $result

    # Add photon noise to the result image.
    addNoise $result $snr
    
    # Delete the in-between results.
    $fftBead del
    $fftPsf  del
    $theoPsf del
}