Running ALPACA from Python Console

Hello, I am trying to run ALPACA from the Python console.

I am accessing the logic with:

import ALPACA
AlpacaLogic = ALPACA.ALPACALogic()
Then I define my paths and directories as inputs for ALPACA batch mode.
I set skipScaling to False

When I try to run:
AlpacaLogic.process(sourceModelPath, sourceLandmarkPath, targetModelDirectory, outputDirectory, skipScaling)

i get the error:

Traceback (most recent call last):
File “”, line 10, in
File “C:/Users/eherbst/AppData/Local/ 5.6.2/”, line 3085, in process
“InputVolume”: inputVolume.GetID(),
AttributeError: ‘str’ object has no attribute ‘GetID’

I see in the code that running Alpaca also requires the ProjectionFactor and Parameters, but if I do not define them as inputs, does it just use the defaults?

hank you,

AlpacaLogic.process is a test utility and doesn’t run the method from the command line. The batch mode tab of the module is intended to handle bundled jobs, maybe if you could describe your use case for running this from the command line I can help find a solution?

I agree with Sara that the best way is probably just to run the batch mode in the UI.

If you want to run the batch mode in Python, you can use the function runLandmarkMultiprocess() in the ALPACALogic. There is a parameter self.parameterDictionary that would have all the required parameters. So far, the default parameters work for most of my cases.You can also check the function onApplyLandmarkMulti() to see how the batch mode runs using the runLandmarkMultiprocess function.

Thank you Sara and Chi!

My use case is that I process a lot of scans (segmentation → landmark transfer via Alpaca → cropping based on landmarks) and since the segmentation and cropping is automated, it would be nice to also automate the Alpaca step to run everything together without manual input.

I will try the runLandmarkMultiprocess function.

Thanks again!

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Hi all,

Thanks for your help!
I got it working with the following function:

def runAlpaca(scapulaModelOutputDir, sourceModelPath, sourceLandmarkPath, landmarkOutputDirectory):
import ALPACA
AlpacaLogic = ALPACA.ALPACALogic()
targetModelDirectory = scapulaModelOutputDir
scalingOption= True
projectionFactor = 0.01
useJSONFormat = True
parameters = { #from Alpaca defaults
“projectionFactor”: 0.01,
“pointDensity”: 1.00,
“normalSearchRadius”: 2,
“FPFHNeighbors”: 100,
“FPFHSearchRadius”: 5.00,
“distanceThreshold”: 3.00,
“maxRANSAC”: 1000000,
“ICPDistanceThreshold”: 1.50,
“alpha”: 2.0,
“beta”: 2.0,
“CPDIterations”: 100,
“CPDTolerance”: 0.001,
“Acceleration”: False,
“BCPDFolder”: “T:/Slicer/bcpd-master/bcpd-master/win”
AlpacaLogic.runLandmarkMultiprocess(sourceModelPath, sourceLandmarkPath, targetModelDirectory, landmarkOutputDirectory, scalingOption, projectionFactor, useJSONFormat, parameters)

I copied all of the default parameters from the GUI, since I couldn’t figure out how to retrieve them from the command line.
Maybe there is a more elegant solution that would update based on user inputs in the GUI, or the plugin’s defaults (in case they ever change).

Also, for projection factor, the default in the GUI is 1.0, but I saw that the code divides this by 100, so I did the same when hard coding the defaults (since it looks like the division happens and then the value is updated in the parameter list).

Setting it directly to 1.0 in the parameter list gave a bad landmark transfer so it looks like this scaling is very important.

Thanks again!

I am glad this worked.

However, what is the purpose of running ALPACA in this way? If you are going to use fixed parameters, I think batch mode will be easier. I thought maybe you are trying to do a parameter sweep (i.e., try many samples with different sets of parameters).

I want to batch process a lot of scans, and am using Alpaca to transfer landmarks to then fit an ROI to each bone and then analyse it. The steps before and after Alpaca are all run from python so it helps to run everything together in an automated way.

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