Commit f9f19ac6 authored by Tung, Chi-Huan's avatar Tung, Chi-Huan
Browse files

fixed input output

parent ac6aa7b6

galaxy/tools/neutrons/mlsans_fit_Yukawa_sq.xml

+7 −5
Original line number Diff line number Diff line 
<tool id="mlsans_fit_Yukawa_sq" name="fit_IQ"  profile="22.04" version="0.1.2">

<tool id="mlsans_fit_Yukawa_sq" name="fit_IQ"  profile="22.04" version="0.1.3">

  <description></description>

    <requirements>

        <container type="docker">code.ornl.gov:4567/ndip/tool-sources/ml-assisted-sans-data-analysis/fit_yukawa_sq:93a0fde1</container>

        <container type="docker">code.ornl.gov:4567/ndip/tool-sources/ml-assisted-sans-data-analysis/fit_yukawa_sq:ac6aa7b6</container>

    </requirements>

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

        python3 /src/curvefit.py -i $input $C $I_inc $sigma $d_sigma $phi $kappa $A || echo python finished && mv output.png $output

        python3 /src/curvefit.py -i $input $C $I_inc $sigma $d_sigma $phi $kappa $A || echo python finished && mv output.png $output && cp /src/output.txt $output2

    ]]></command>

    <inputs>

        <param name="input" type="text" value="/src/example_IQ.csv" optional="false" label="ASCII data"/>

        <param name="input" type="data" optional="false" label="ASCII data"/>

        <param name="C" type="text" value="4000 3500 4500" label="C" optional="false" help="Contrast"/>

        <param name="I_inc" type="text" value="0.5 0.1 2" label="I_inc" optional="false" help="Incoherent background"/>

        <param name="sigma" type="text" value="1 0.9 1.1" label="σ" optional="false" help="Particle diameter"/>
@@ -18,7 +18,9 @@ 
    </inputs>

	

    <outputs>

        <data name="output" format="png" label="fitting results">

        <data name="output" format="png" label="fitting results plot">

        </data>

        <data name="output2" format="txt" label="fitting results">

        </data>

    </outputs>

    <help><![CDATA[

galaxy/tools/neutrons/mlsans_fit_Yukawa_sq_backup.xml

0 → 100644
+30 −0
Original line number Diff line number Diff line 
<tool id="mlsans_fit_Yukawa_sq" name="fit_IQ"  profile="22.04" version="0.1.3">

  <description></description>

    <requirements>

        <container type="docker">code.ornl.gov:4567/ndip/tool-sources/ml-assisted-sans-data-analysis/fit_yukawa_sq:ac6aa7b6</container>

    </requirements>

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

        python3 /src/curvefit.py -i $input $C $I_inc $sigma $d_sigma $phi $kappa $A || echo python finished && mv output.png $output && cp /src/output.txt $output2

    ]]></command>

    <inputs>

        <param name="input" type="text" value="/src/example_IQ.csv" optional="false" label="ASCII data"/>

        <param name="C" type="text" value="4000 3500 4500" label="C" optional="false" help="Contrast"/>

        <param name="I_inc" type="text" value="0.5 0.1 2" label="I_inc" optional="false" help="Incoherent background"/>

        <param name="sigma" type="text" value="1 0.9 1.1" label="σ" optional="false" help="Particle diameter"/>

        <param name="d_sigma" type="text" value="0.07 0.02 0.1" label="d_σ" optional="false" help="Particle size polydispersity"/>

        <param name="phi" type="text" value="0.1 0.05 0.25" label="Φ" optional="false" help="Volume fraction"/>

        <param name="kappa" type="text" value="0.2 0.1 0.3" label="1/κD" optional="false" help="Screening constant"/>

        <param name="A" type="text" value="10 1 20" label="βA" optional="false" help="Repulsion strength"/>

    </inputs>

	

    <outputs>

        <data name="output" format="png" label="fitting results plot">

        </data>

        <data name="output2" format="txt" label="fitting results">

        </data>

    </outputs>

    <help><![CDATA[

        Fit the input I(Q) curve. Initial guess, lower bound and upper bound are separated using spaces.

]]></help>

</tool>

src/curvefit.py

+3 −3
Original line number Diff line number Diff line
@@ -140,10 +140,10 @@ def fit(initial_guess, file_name): 
    with open('output.txt', 'a') as f:

        for param in result.params.values():

            if param.stderr is None: 

                string = "%s:  %f +/- undetermined (init = %f)" % (param.name, param.value, param.init_value)

                string = "%s:  %f +/- undetermined (init = %f)\n" % (param.name, param.value, param.init_value)

            else:

                string = "%s:  %f +/- %f (init = %f)" % (param.name, param.value, param.stderr, param.init_value)

            print(string)

                string = "%s:  %f +/- %f (init = %f)\n" % (param.name, param.value, param.stderr, param.init_value)

            f.write(string)





if __name__ == '__main__':