Returning a vector from CLI module

Development
1

Hello Developers.

I am developing a CLI module and calling it from my scripted module using “slicer.cli.run” . I can parse the arguments from my scripted module to CLI module but I failed to get the returning arguments from my CLI module.

I am trying to copy fudicial registration module but unfortunately I wasn’t able to get the returning argument in my scripted module. I am missing simething, it might be very basic, but I have wasted alot of time in it.

My XML is:

<?xml version="1.0" encoding="utf-8"?>
Examples CLI_test 0.0.1 http://www.example.com/Slicer/Modules/CLI_test Slicer FirstName LastName (Institution), FirstName LastName (Institution) This work was partially funded by NIH grant NXNNXXNNNNNN-NNXN IO sigmas sigmas s output 
  <label>Sigmas</label>
  <description><![CDATA[A double value (in units of mm) passed to the algorithm]]></description>
     </float-vector>

<double>
  <name>rms</name>
  <longflag>rms</longflag>
  <description><![CDATA[Display RMS Error.]]></description>
  <flag>R</flag>
  <label>RMS Error</label>
  <channel>output</channel>
  <default>0.1</default>
</double>

The part of updating rms value in my CLI .cpp code is:

rms=42.0 ;
std::ofstream rts;
rts.open(returnParameterFile.c_str() );
rts << “rms=” << rms << std::endl;
rts.close();

I dont know how to get this “rms” value in my scripted module (python code). Thank you in advance

2

Just to be clear, If I run my CLI module as standalone program it does generate an output text file, my question is, how can I get the output if I call my CLI from scripted module with slicer.cli.run command.

Thank you.

3

Return values are stored in the parameter node and you can retrieve it using GetParameterAsString() method. For example:

parameterNode = slicer.util.getNode('Execution Model Tour')
returnedRmsValue = float(parameterNode.GetParameterAsString('rms'))
4

Thank you for you reply Andras, I have tried this command, the problem is my ‘rms’ variable doesn’t get updated. its just returning the same initial value.

Ideally, inital rms value should go into my CLI module , it should get updated, and I should get the updated variable.

this is the python code from where I am calling my CLI

module = slicer.modules.cli_test

rms=5.0
a=(np.random.randint(0, 100, size=(30, 10, 2)) ).tolist()

cliParams = {
  'sigmas' : a,
  'rms' : rms,


}

cliNode = slicer.cli.run(module, None, cliParams, wait_for_completion=True)

returnedRmsValue = float(cliNode.GetParameterAsString('rms'))
print(returnedRmsValue)

The returned RMS value should be 49, but it is still giving 5.
Am I missing something?

5

A parameter can be either input or output, defined by the channel element. For example, <channel>output</channel> means an output parameter.

6

yes, I have defined the parameter as output. (xml attached in my first post). Even then it is not updating.

7

It works for me with the ExecutionModelTour test module. See how to correctly write output parameters here:

There are no whitespaces in your code above, maybe that breaks the output file parsing.

8

Thank you fro your response Andras, I have tried the exact same thing. Even hardcoded the text, it is still returning the same value.

Am I making any mistake in calling a CLI?

cliNode = slicer.cli.run(module, None, cliParams, wait_for_completion=True)

parameters being:

rms=5.0
a=(np.random.randint(0, 100, size=(30, 10, 2)) ).tolist()
sigmaout=23.0
cliParams = {
  'sigmas' : a,
  'rms' : rms,
  'sigmaout' : sigmaout

}
9

Thank you Andras, it worked. there were some other problems. Thank you for your help

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