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?

You can check this FAQ for commonly known errors and how to fix them.

The fastr toolbox has a method to trace back errors. For more details, see the fastr documentation. If you want to know the exact error that occured in a job, make sure you trace back to a single sink and single sample, e.g. ``fastr trace $RUNDIR/__sink_data__.json –sinks sink_5 –sample sample_1_1 ``. See the User Manual chapter for more info.

Error: fastr.exceptions.FastrValueError: [...] FastrValueError from `` ``.../fastr/execution/job.py line 834: Output values are not valid!

This a general error fastr returns when a job failed: since there is no output generated, the output values are obviously not valid for what fastr expected. Hence that does not give you any input on why the job failed. What you want is the actual error that occured in the tool, e.g., the Python error. If you debug the fastr network, see above, use the fastr trace command to trace back the error of a specific sink and a specific sample to track down the exact tool error, e.g., the Python error.

Error: File "H5FDsec2.c", line 941, in H5FD_sec2_lock unable to lock file, errno = 37, error message = 'No locks available'

Known HDF5 error, see also https://github.com/h5py/h5py/issues/1101. Can be solved by setting the HDF5_USE_FILE_LOCKING environment variable to ‘FALSE’, e.g. adding export HDF5_USE_FILE_LOCKING=’FALSE’ to your ~..bashrc on Linux.

Error: Failed building wheel for cryptography (occurs often on BIGR cluster)

This bug can be caused when using pyOpenSSL 22.1.0 or recent cryptography versions on the BIGR cluster. Cryptography 3.4.7 and PyOpenSSL 20.0.1 should work, so install those (in that order) before installing WORC.

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 the specific WORC tutorial on using your own features: https://github.com/MStarmans91/WORCtutorial/Extra_tutorials/WORCTutorialBasic_OwnFeatures.py. 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.:

.. code-block:: python

feature_dict = {‘Patient1’: ‘/path/to/featurespatient1.hdf5’, ‘Patient2’: ‘/path/to/someotherrandandomfolderwith/featurespatient2.hdf5’}

How to change the temporary and output folders?

WORC makes use of the fastr workflow engine to manage and execute the experiment, and thus also to manage and produce the output. These folders can be configured in the fastr config (https://fastr.readthedocs.io/en/stable/static/file_description.html#config-file). The fastr config files can be found in a hidden folder .fastr in your home folder. WORC adds an additional config file to the config.d folder of fastr: https://github.com/MStarmans91/WORC/blob/master/WORC/fastrconfig/WORC_config.py.

The two mounts that determine the temporary and output folders and thus which you have to change are: - Temporary output: mounts['tmp'] in the ~/.fastr/config.py file - Final output: mounts['output'] in the ~/.fastr/config.d/WORC_config.py file

How can I get the performance on the validation dataset?

The performance of the top 1 workflow is stored in the fitted estimators in the estimator_all_0.hdf5 file:

data = pd.read_hdf("estimator_all_0.hdf5")
data = data[list(data.keys())[0]]

validation_performance = list()
# Iterate over all train-test cross validations
for clf in data.classifiers:
    validation_performance.append(clf.best_score_)

My jobs on the BIGR cluster get cancelled due to memory errors

You can adjust the memory for various jobs through changing the values in the WORC.fastr_memory_parameters dictionary (accesible in SimpleWORC and BasicWORC through _worc.fastr_memory_parameters.) The fit_and_score job memory can be adjusted through the WORC HyperOptimization config, see Configuration chapter.