pcntoolkit.util.output
======================
.. py:module:: pcntoolkit.util.output
Classes
-------
.. autoapisummary::
pcntoolkit.util.output.Errors
pcntoolkit.util.output.Messages
pcntoolkit.util.output.Output
pcntoolkit.util.output.Warnings
Module Contents
---------------
.. py:class:: Errors
.. py:attribute:: BLR_ERROR_NO_DESIGN_MATRIX_CREATED
:value: 'No design matrix created'
.. py:attribute:: BLR_HYPERPARAMETER_VECTOR_INVALID_LENGTH
:value: 'Hyperparameter vector invalid length'
.. py:attribute:: BLR_MODEL_NOT_FITTED
:value: 'Model must be fitted before computing log probabilities'
.. py:attribute:: BLR_X_NOT_PROVIDED
:value: 'X is not provided'
.. py:attribute:: ENSURE_POSITIVE_DISTRIBUTION
:value: 'Distribution for {name} needs to be positive.'
.. py:attribute:: ERROR_ARGUMENT_SPECIFIED_TWICE
:value: 'Argument {key} is specified twice.'
.. py:attribute:: ERROR_BASIS_FUNCTION_NOT_FITTED
:value: 'Basis function is not fitted. Please fit the basis function first.'
.. py:attribute:: ERROR_BATCH_EFFECTS_NOT_LIST
:value: 'Items of the batch_effect dict be a list or a string, not {batch_effect_type}'
.. py:attribute:: ERROR_BATCH_SIZE_AND_N_BATCHES_MISMATCH
:value: 'Batch size ({batch_size}) and number of batches ({n_batches}) are both specified, but do not...
.. py:attribute:: ERROR_BLR_CG_NOT_SUPPORTED_WITH_WARP
:value: "The 'cg' optimizer requires analytical gradients, which are not implemented for warped models....
.. py:attribute:: ERROR_BLR_HYPERPARAMETER_VECTOR_INVALID_LENGTH
:value: 'Hyperparameter vector invalid length'
.. py:attribute:: ERROR_BLR_PENALTY_NOT_RECOGNIZED
:value: "Requested penalty ({penalty}) not recognized, choose between 'L1' or 'L2'."
.. py:attribute:: ERROR_BLR_POWELL
:value: "Powell optimizer failed. We recommend running your code again and setting optimizer='l-bfgs-b'."
.. py:attribute:: ERROR_BLR_TRANSFER_NOT_IMPLEMENTED
:value: 'BLR transfer not implemented'
.. py:attribute:: ERROR_BLR_VAR_X_NOT_PROVIDED
:value: 'Variance of covariates (var_X) is required for models with variance.'
.. py:attribute:: ERROR_BLR_WARPS_NOT_PROVIDED
:value: 'A list of warp functions is required'
.. py:attribute:: ERROR_CDF_SHAPE
:value: 'CDF shape {cdf_shape} does not match data shape {data_shape}'
.. py:attribute:: ERROR_CROSS_VALIDATION_FOLDS
:value: 'If cross-validation is enabled, cv_folds must be greater than 1'
.. py:attribute:: ERROR_DATA_MUST_BE_1D
:value: 'Data must be a 1D array or a N-dimensional array with a single column'
.. py:attribute:: ERROR_ENVIRONMENT_NOT_FOUND
:value: 'Environment {environment} not found. Please specify the path to the python environment using...
.. py:attribute:: ERROR_FILE_NOT_FOUND
:value: 'File not found: {path}'
.. py:attribute:: ERROR_HBRDATA_X_NOT_PROVIDED
:value: 'X must be provided'
.. py:attribute:: ERROR_HBR_COULD_NOT_LOAD_IDATA
:value: 'Could not load idata from {path}'
.. py:attribute:: ERROR_HBR_FITTED_BUT_NO_IDATA
:value: 'HBR model is fitted but does not have idata. This should not happen.'
.. py:attribute:: ERROR_HBR_Y_NOT_PROVIDED
:value: 'y must be provided for z-score computation'
.. py:attribute:: ERROR_MODEL_NOT_FITTED
:value: 'Model needs to be fitted before it can be transferred'
.. py:attribute:: ERROR_MULTIPLE_COVARIATE_DIMS
:value: 'Multiple covariate dimensions found: {covariate_dims}'
.. py:attribute:: ERROR_NO_ENVIRONMENT_SPECIFIED
:value: 'No python environment specified. Please specify the path to the python environment using the...
.. py:attribute:: ERROR_PARSING_TIME_LIMIT
:value: 'Cannot parse {time_limit_str} as time limit'
.. py:attribute:: ERROR_PREDICT_DATA_NOT_SUPPORTED_FOR_CROSS_VALIDATION
:value: 'Predict with cross-validation is not supported. Please use fit_predict instead.'
.. py:attribute:: ERROR_PREDICT_DATA_REQUIRED
:value: 'Predict data is required for fit_predict without cross-validation'
.. py:attribute:: ERROR_PREDICT_DATA_REQUIRED_FOR_FIT_PREDICT_WITHOUT_CROSS_VALIDATION
:value: 'Predict data is required for fit_predict without cross-validation'
.. py:attribute:: ERROR_SCALER_NOT_FITTED
:value: 'Scaler must be fitted before {method}'
.. py:attribute:: ERROR_SCALER_TYPE_NOT_FOUND
:value: "Dictionary must contain 'scaler_type' key"
.. py:attribute:: ERROR_SOURCE_ARRAY_NOT_FOUND
:value: 'Source array {source_array_name} does not exist in the data.'
.. py:attribute:: ERROR_SUBMITTING_JOB
:value: 'Error submitting job {job_id}: {stderr}'
.. py:attribute:: ERROR_UNKNOWN_CLASS
:value: 'Unknown class {class_name}'
.. py:attribute:: ERROR_UNKNOWN_DISTRIBUTION
:value: 'Unknown distribution ({dist_name})'
.. py:attribute:: ERROR_UNKNOWN_FUNCTION
:value: 'Unknown function {func}'
.. py:attribute:: ERROR_UNKNOWN_LIKELIHOOD
:value: 'Unsupported likelihood ({likelihood})'
.. py:attribute:: ERROR_UNKNOWN_MAPPING
:value: 'Unknown mapping ({mapping})'
.. py:attribute:: ERROR_UNKNOWN_SCALER_TYPE
:value: 'Undefined scaler type: {scaler_type}'
.. py:attribute:: ERROR_WARP_STRING_INVALID
:value: 'Invalid warp string: {warp_string}'
.. py:attribute:: ERROR_Y_NOT_FOUND
:value: 'y not found in data'
.. py:attribute:: ERROR_ZSCORES_INVERSE
:value: 'Z-scores inverse has invalid shape: Z_shape={Z_shape}, X_shape={X_shape}'
.. py:attribute:: HBR_MODEL_NOT_FITTED
:value: 'HBR model is not fitted'
.. py:attribute:: INVALID_ENVIRONMENT
:value: 'The python environment {environment} is invalid because it has no /bin/python file. Please...
.. py:attribute:: NORMATIVE_MODEL_CONFIGURATION_PROBLEMS
:value: Multiline-String
.. raw:: html
Show Value
.. code-block:: python
"""The following problems have been detected in the normative model configuration:
{problems}"""
.. raw:: html
Show Value
.. code-block:: python
"""The following problems have been detected in the regression model configuration:
{problems}"""
.. raw:: html
Show Value
.. code-block:: python
"""Dataset "{name}" created.
- {n_observations} observations
- {n_subjects} unique subjects
- {n_covariates} covariates
- {n_response_vars} response variables
- {n_batch_effects} batch effects:
{batch_effects}
"""
.. raw:: html
Show Value
.. code-block:: python
"""Execution of callable failed, attempt {attempt} of {total} with error:
{error}"""
.. raw:: html
Show Value
.. code-block:: python
"""
---------------------------------------------------------
PCNtoolkit Job Status Monitor ®
---------------------------------------------------------
Task ID: {task_id}
---------------------------------------------------------
Job ID Name State Time Nodes
---------------------------------------------------------
"""
.. raw:: html
Show Value
.. code-block:: python
"""
---------------------------------------------------------
Total active jobs: {total_active_jobs}
Total completed jobs: {total_completed_jobs}
Total failed jobs: {total_failed_jobs}
---------------------------------------------------------
"""
.. raw:: html
Show Value
.. code-block:: python
"""Loading runner state from:
{runner_file}"""
.. raw:: html
Show Value
.. code-block:: python
"""Log directory created:
{log_dir}"""
.. raw:: html
Show Value
.. code-block:: python
"""
---------------------------------------------------------
No more running jobs!
---------------------------------------------------------
"""
.. raw:: html
Show Value
.. code-block:: python
"""Runner loaded
---------------------------------------------------------Active jobs: {n_active_jobs}
Finished jobs: {n_finished_jobs}
Failed jobs: {n_failed_jobs}
---------------------------------------------------------"""
.. raw:: html
Show Value
.. code-block:: python
"""Saving centiles to:
{save_dir}."""
.. raw:: html
Show Value
.. code-block:: python
"""Saving model to:
{save_dir}."""
.. raw:: html
Show Value
.. code-block:: python
"""Saving results to:
{save_dir}."""
.. raw:: html
Show Value
.. code-block:: python
"""Saving runner state to:
{runner_file}"""
.. raw:: html
Show Value
.. code-block:: python
"""Saving statistics to:
{save_dir}."""
.. raw:: html
Show Value
.. code-block:: python
"""Saving z-scores to:
{save_dir}."""
.. raw:: html
Show Value
.. code-block:: python
"""Temporary directory created:
{temp_dir}"""
.. raw:: html
Show Value
.. code-block:: python
"""Posterior estimation failed:
{error}.
The optimizer could not find a stable solution. Retrying optimization."""
.. raw:: html