FAQ

Installation

Error: ModuleNotFoundError: No module named 'numpy'

Some versions of several packages that WORC uses, such as PyWavelets and PyRadiomics, require numpy during their installation. To solve this issue, simply first install numpy before installing WORC or any of the dependencies , i.e. pip install numpy or conda install numpy when using Anaconda.

Execution errors

My experiment crashed, where to begin looking for errors?

The fastr toolbox has a method to trace back errors. For more details, see the fastr documentation.

Error: WORC.addexceptions.WORCValueError: First column in the file given to SimpleWORC().labels_from_this_file(**) needs to be named Patient.

This means that your label file, i.e. in which the label to be predicted for each patient is given, is not formatted correctly. Please see the Configuration chapter, or the WORC Tutorial Github for an example.

Error: WORC.addexceptions.WORCKeyError: 'No entry found in labeling for feature file .../feat_out_0.hdf5.'

This means for this specific file (../feat_out_0.hdf5), WORC could not find a label in your label file. Please make sure that one of the Patient IDs from your label file occurs in the filename of your inputs. For example, when using the example label file from the WORC tutorial, if your Patient ID is not listed in column 1, this error will occur.

Error: File "...\lib\site-packages\numpy\lib\function_base.py", line 4406, `` in delete keep[obj,] = False`` IndexError: arrays used as indices must be of integer (or boolean) type

This is an error in PyRadiomics 3.0, see also this issue. It has currently to be manually solved by within the PyRadiomics package, in the glcm, gldm, glrlm, glszm and ngtdm functions, searching for the line starting with emptyGrayLevels =. After that, there will be a line similar to P_ngtdm = numpy.delete(P_ngtdm, emptyGrayLevels, 1). Before that line, add a conditional if list(emptyGrayLevels):, e.g. for the NGTDM:

if list(emptyGrayLevels):
  P_ngtdm = numpy.delete(P_ngtdm, emptyGrayLevels, 1)

See also my fork of PyRadiomics, which you can also install to fix the issue: https://github.com/MStarmans91/pyradiomics.

Other

I am working on the BIGR cluster and would like some jobs to be submitted to different queues

Unfortunately, fastr does not support giving a queue argument per job. In general, we assume you would like all your jobs to be run on the day queue, which you can set as the default, and only the classify job on the week queue. The only solution we currently have is to manually hack this into fastr:

  1. Go to the installation of the fastr package in your (virtual) environment.

  2. Open the fastr/resources/plugins/executionplugins/drmaaplugin.py script.

  3. Search for the line if queue is None: and replace that if loop

with the following:

if queue is None:
    if 'classify' in command:
        fastr.log.info('Detected classify in command: submitting to week queue')
        queue = 'week'
    elif any('classify' in a for a in arguments):
        fastr.log.info('Detected classify in arguments: submitting to week queue')
        queue = 'week'
    else:
        queue = self.default_queue

Can I use my own features instead of the standard WORC features?

WORC also includes an option to use your own features instead of the default features included. WORC will than simply start at the data mining (e.g. classification, regression) step, and thus after the normal feature extraction. This requires three things

1. Convert your features to the default WORC format

WORC expects your features per patient in a .hdf5 file, containing a pandas series with at least a feature_values and a feature_labels object. The feature_values object should be a list containing your feature values, the feature_labels object a list with the corresponding featuree labels. Below an example on how to create such a series.

# Dummy variables
feature_values = [1, 1.5, 25, 8]
feature_labels = ['label_feature_1', 'label_feature_2', 'label_feature_3',
                  'label_feature_4']

# Output filename
output = 'test.hdf5'

# Converting features to pandas series and saving
panda_data = pd.Series([feature_values,
                        feature_labels],
                       index=['feature_values', 'feature_labels'],
                       name='Image features'
                       )

panda_data.to_hdf(output, 'image_features')

2. Alter feature selection on the feature labels

WORC by default includes groupwise feature selection, were groups of features are randomly turned on or off. Since your feature labels are probably not in the default included values, you should turn this of. This can be done by setting the config['Featsel']['GroupwiseSearch'] to "False".

Alternatively, you can use default feature labels in WORC and still use the groupwise feature selection. This is relatively simple: for example, shape features are recognized by looking for "sf_" in the feature label name. To see which labels are exactly used, please see WORC.featureprocessing.SelectGroups and the SelectFeatGroup section in the Config chapter.

3. Tell WORC to use your feature and not compute the default ones

To this end, SimpleWORC, and therefore also BasicWORC, include the function features_from_this_directory(). See also the quick start guide. As explained in the WORCTutorial, a default structure of your featuresdatadir folder is expected in this function: there should be a subfolder for each patient, in which the feature file should be. The feature file can have a fixed name, but wildcard are allowed in the search, see also the documentation of the features_from_this_directory() function.

Altneratively, when using BasicWORC, you can append dictionaries to the features_train object. Each dictionary you append should have as keys the patient names, and as values the paths to the feature files, e.g. feature_dict = {'Patient1': '/path/to/featurespatient1.hdf5', 'Patient2': '/path/to/someotherrandandomfolderwith/featurespatient2.hdf5'...}.