Commit 2544d3f6 authored by Smith, Robert's avatar Smith, Robert Committed by Yakubov, Sergey
Browse files

Added IMAGINE-X tools 

Added image converter and occupancy tools for IMAGINE-X. Also updated
image generator.
parent 5291243a

tools/neutrons/imaginex_image_converter.xml

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<tool id="imaginex_image_converter" name="IMAGINE-X image converter"  profile="22.05" version="0.1.0-dev" python_template_version="3.5">

  <requirements>

    <container type="docker">code.ornl.gov:4567/dnp-computational-project/data-reduction-ndip-tools/jpeg-file-converter/production/main:0.0.3</container>

  </requirements>

    <command detect_errors="exit_code"><![CDATA[



		mkdir in ;

		mkdir out ; 



		#for $input in $inputs

		    mv $input in/$input.element_identifier ;

		#end for



		python /convert.py --input in --output out --type $type ;



    ]]></command>

    <inputs>

    

		<param format="dat" multiple="true" name="inputs" type="data" label="Anger camera input files" />

		<param name="type" type="select" optional="false" value="TIFF" label="Output Format" help="Image file format for output files.">

			<option value="TIFF">TIFF</option>

			<option value="PNG">PNG</option>

		</param>



    </inputs>

    <outputs>

	<collection name="output_files" type="list" label="Output Images">

	    <discover_datasets pattern="(?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;[^\._]+)$" directory="out" />

	</collection>

    </outputs>

    <help><![CDATA[

        Converts input files into .pngs for use with peak finding tool.

    ]]></help>

</tool>

tools/neutrons/imaginex_image_generator.xml

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<tool id="imaginex_image_generator" name="IMAGINE-X image generator"  profile="22.05" version="1.0.0" python_template_version="3.5">

<tool id="imaginex_image_generator" name="IMAGINE-X image generator"  profile="22.05" version="0.1.0-dev" python_template_version="3.5">

  <requirements>

    <container type="docker">code.ornl.gov:4567/dnp-computational-project/instrument/brave-image-generator:latest</container>

    <container type="docker">code.ornl.gov:4567/dnp-computational-project/data-reduction-ndip-tools/imagine-image-generator/production/main:0.0.3</container>

  </requirements>

    <command detect_errors="exit_code"><![CDATA[

        mkdir output ;
@@ -11,14 +11,14 @@ 
	        #set $timeOption = ""

	    #end if

	    

	    python /opt/image_counts.py --input_file $input --output_dir output $timeOption --wavelength_max $wavelengthMax --wavelength_min $wavelengthMin ;

	    python /image_counts.py --input_file $input --output_dir output $timeOption --wavelength_max $wavelengthMax --wavelength_min $wavelengthMin ;



    ]]></command>

    <inputs>

    

        <param name="input" type="data" format="h5" label="Input File">

	    </param>

	    <param name="wavelengthMin" type="float" value="1.0" label="Max Wavelength"> 

	    <param name="wavelengthMin" type="float" value="1.0" label="Min Wavelength"> 

		</param>

		<param name="wavelengthMax" type="float" value="3.5" label="Max Wavelength"> 

		</param>
@@ -38,6 +38,6 @@ 
	</collection>

    </outputs>

    <help><![CDATA[

        Iage generation for IMAGINE-X beamline data reduction.

        Image generation for IMAGINE-X beamline data reduction.

    ]]></help>

</tool>

tools/neutrons/imaginex_occupancy.xml

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<tool id="imaginex_occupancy-dev" name="Occupancy Fitting"  profile="22.05" version="0.1.1-dev" python_template_version="3.5">

  <requirements>

    <container type="docker">code.ornl.gov:4567/dnp-computational-project/instrument/occupancy:test3</container>

  </requirements>

    <command detect_errors="exit_code"><![CDATA[



		mkdir output ;



		ls / ;



		ls /occupancy ;



	    #if $xray == True

	    	#set $xrayOption = "--xray "

	    #else

	        #set $xrayOption = ""

	    #end if



	    #if $full == True

	    	#set $fullOption = "--full "

	    #else

	        #set $fullOption = ""

	    #end if



	    #if $biomt == True

	    	#set $biomtOption = "--biomt "

	    #else

	        #set $biomtOption = ""

	    #end if



	    #if $occFree == True

	    	#set $occFreeOption = "--occ_free "

	    #else

	        #set $occFreeOption = ""

	    #end if



		#if $typeCond.type == "reflections"

			#set $secondFile = "--reflections " + str($typeCond.reflectionsFile) + " --miller_array " + str($typeCond.miller)

		#else

			#set $secondFile = "--ref_pdb " + str($typeCond.referenceFile) + " --d_min  " + str($typeCond.dMin)

		#end if



		python /occupancy/occupancy.py $input output/output.pdb $xrayOption $fullOption $biomtOption $occFreeOption $secondFile ;



    ]]></command>

    <inputs>



        <param name="input" type="data" format="pdb" label="Input File">

	    </param>

	    <param name="xray" type="boolean" checked="false" label="Use x-ray structure factors">

		</param>

	    <param name="full" type="boolean" checked="false" label="Full occupancy refinement (heavy atoms + H + D)">

		</param>

	    <param name="biomt" type="boolean" checked="false" label="Expand BIOMT records">

		</param>

	    <param name="occFree" type="boolean" checked="false" label="Do NOT constrain occupancy between [0,1]">

		</param>

		<conditional name="typeCond">

			<param name="type" type="select" optional="false" value="reflections" label="Type" help="Which type of secondary file to use.">

				<option value="reflections">Reflections file</option>

				<option value="reference">Reference protons file</option>

			</param>

			<when value="reflections">

		        <param name="reflectionsFile" type="data" format="cif" label="Reflections File">

			    </param>

			    <param name="miller" type="text" value="" label="Miller Array Column Name" help="Must be a column from the Reflections File above.">

				</param>

			</when>

			<when value="reference">

		        <param name="referenceFile" type="data" format="pdb" label="Reference Protons File">

			    </param>

				<param name="dMin" type="float" value="2" label="d min" help="Resolution [Å]">

				</param>

			</when>

		</conditional>



    </inputs>

    <outputs>

		<data format="pdb" name="output" from_work_dir="output/output.pdb" />

    </outputs>

    <help><![CDATA[

        Fit occupancies to neutron data.

    ]]></help>

</tool>