pcntoolkit.util.output

Classes

Errors
Messages
Output
Warnings

Module Contents

class Errors

BLR_ERROR_NO_DESIGN_MATRIX_CREATED = 'No design matrix created'

BLR_HYPERPARAMETER_VECTOR_INVALID_LENGTH = 'Hyperparameter vector invalid length'

BLR_MODEL_NOT_FITTED = 'Model must be fitted before computing log probabilities'

BLR_X_NOT_PROVIDED = 'X is not provided'

ENSURE_POSITIVE_DISTRIBUTION = 'Distribution for {name} needs to be positive.'

ERROR_ARGUMENT_SPECIFIED_TWICE = 'Argument {key} is specified twice.'

ERROR_BASIS_FUNCTION_NOT_FITTED = 'Basis function is not fitted. Please fit the basis function first.'

ERROR_BATCH_EFFECTS_NOT_LIST = 'Items of the batch_effect dict be a list or a string, not {batch_effect_type}'

ERROR_BATCH_SIZE_AND_N_BATCHES_MISMATCH = 'Batch size ({batch_size}) and number of batches ({n_batches}) are both specified, but do not...

ERROR_BLR_CG_NOT_SUPPORTED_WITH_WARP = "The 'cg' optimizer requires analytical gradients, which are not implemented for warped models....

ERROR_BLR_HYPERPARAMETER_VECTOR_INVALID_LENGTH = 'Hyperparameter vector invalid length'

ERROR_BLR_PENALTY_NOT_RECOGNIZED = "Requested penalty ({penalty}) not recognized, choose between 'L1' or 'L2'."

ERROR_BLR_POWELL = "Powell optimizer failed. We recommend running your code again and setting optimizer='l-bfgs-b'."

ERROR_BLR_TRANSFER_NOT_IMPLEMENTED = 'BLR transfer not implemented'

ERROR_BLR_VAR_X_NOT_PROVIDED = 'Variance of covariates (var_X) is required for models with variance.'

ERROR_BLR_WARPS_NOT_PROVIDED = 'A list of warp functions is required'

ERROR_CDF_SHAPE = 'CDF shape {cdf_shape} does not match data shape {data_shape}'

ERROR_CROSS_VALIDATION_FOLDS = 'If cross-validation is enabled, cv_folds must be greater than 1'

ERROR_DATA_MUST_BE_1D = 'Data must be a 1D array or a N-dimensional array with a single column'

ERROR_ENVIRONMENT_NOT_FOUND = 'Environment {environment} not found. Please specify the path to the python environment using...

ERROR_FILE_NOT_FOUND = 'File not found: {path}'

ERROR_HBRDATA_X_NOT_PROVIDED = 'X must be provided'

ERROR_HBR_COULD_NOT_LOAD_IDATA = 'Could not load idata from {path}'

ERROR_HBR_FITTED_BUT_NO_IDATA = 'HBR model is fitted but does not have idata. This should not happen.'

ERROR_HBR_Y_NOT_PROVIDED = 'y must be provided for z-score computation'

ERROR_MODEL_NOT_FITTED = 'Model needs to be fitted before it can be transferred'

ERROR_MULTIPLE_COVARIATE_DIMS = 'Multiple covariate dimensions found: {covariate_dims}'

ERROR_NO_ENVIRONMENT_SPECIFIED = 'No python environment specified. Please specify the path to the python environment using the...

ERROR_PARSING_TIME_LIMIT = 'Cannot parse {time_limit_str} as time limit'

ERROR_PREDICT_DATA_NOT_SUPPORTED_FOR_CROSS_VALIDATION = 'Predict with cross-validation is not supported. Please use fit_predict instead.'

ERROR_PREDICT_DATA_REQUIRED = 'Predict data is required for fit_predict without cross-validation'

ERROR_PREDICT_DATA_REQUIRED_FOR_FIT_PREDICT_WITHOUT_CROSS_VALIDATION = 'Predict data is required for fit_predict without cross-validation'

ERROR_SCALER_NOT_FITTED = 'Scaler must be fitted before {method}'

ERROR_SCALER_TYPE_NOT_FOUND = "Dictionary must contain 'scaler_type' key"

ERROR_SOURCE_ARRAY_NOT_FOUND = 'Source array {source_array_name} does not exist in the data.'

ERROR_SUBMITTING_JOB = 'Error submitting job {job_id}: {stderr}'

ERROR_UNKNOWN_CLASS = 'Unknown class {class_name}'

ERROR_UNKNOWN_DISTRIBUTION = 'Unknown distribution ({dist_name})'

ERROR_UNKNOWN_FUNCTION = 'Unknown function {func}'

ERROR_UNKNOWN_LIKELIHOOD = 'Unsupported likelihood ({likelihood})'

ERROR_UNKNOWN_MAPPING = 'Unknown mapping ({mapping})'

ERROR_UNKNOWN_SCALER_TYPE = 'Undefined scaler type: {scaler_type}'

ERROR_WARP_STRING_INVALID = 'Invalid warp string: {warp_string}'

ERROR_Y_NOT_FOUND = 'y not found in data'

ERROR_ZSCORES_INVERSE = 'Z-scores inverse has invalid shape: Z_shape={Z_shape}, X_shape={X_shape}'

HBR_MODEL_NOT_FITTED = 'HBR model is not fitted'

INVALID_ENVIRONMENT = 'The python environment {environment} is invalid because it has no /bin/python file. Please...

NORMATIVE_MODEL_CONFIGURATION_PROBLEMS = Multiline-String

Show Value

"""The following problems have been detected in the normative model configuration:
{problems}"""

NO_FLOAT_DATA_TYPE = 'Only float data types currently handled, not {data_type}'

OFFSETS_NOT_1D = 'Offsets must be a 1-d array or list'

OFFSET_NOT_VALID = 'Invalid list of offsets provided'

REGRESSION_MODEL_CONFIGURATION_PROBLEMS = Multiline-String

Show Value

"""The following problems have been detected in the regression model configuration:
{problems}"""

SAMPLE_BATCH_EFFECTS = 'Cannot sample {n_samples} batch effects, because some batch effects have more levels than the...

UNKNOWN_FILE_TYPE = 'Unknown file type: {filename}'

WB_COMMAND_FAILED = 'wb_command failed with error: {error}'

WB_COMMAND_NOT_FOUND = 'wb_command not found in PATH'

class Messages

BLR_HYPERPARAMETERS_HAVE_NOT_CHANGED = 'Hyperparameters have not changed, exiting'

BLR_RESTARTING_ESTIMATION_AT_HYP = 'Restarting estimation at hyp = {hyp}, due to: {e}'

COMPUTING_CENTILES = 'Computing centiles for {n_models} response variables.'

COMPUTING_CENTILES_MODEL = 'Computing centiles for {model_name}.'

COMPUTING_LOGP = 'Computing log-probabilities for {n_models} response variables.'

COMPUTING_LOGP_MODEL = 'Computing log-probabilities for {model_name}.'

COMPUTING_YHAT = 'Computing yhat for {n_models} response variables.'

COMPUTING_YHAT_MODEL = 'Computing yhat for {model_name}.'

COMPUTING_ZSCORES = 'Computing z-scores for {n_models} response variables.'

COMPUTING_ZSCORES_MODEL = 'Computing z-scores for {model_name}.'

DATASET_CREATED = Multiline-String

Show Value

"""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}
    """

EXECUTING_CALLABLE = 'Executing callable, attempt {attempt} of {total}.'

EXECUTION_FAILED = Multiline-String

Show Value

"""Execution of callable failed, attempt {attempt} of {total} with error:
{error}"""

EXECUTION_SUCCESSFUL = 'Execution of callable successful, attempt {attempt} of {total}.'

EXTRACTING_CIFTI_SURFACE_DATA = 'Extracting cifti surface data to {outstem} ...'

EXTRACTING_CIFTI_VOLUME_DATA = 'Extracting cifti volume data to {niiname} ...'

FITTING_AND_PREDICTING_MODEL = 'Fitting and predicting model for {model_name}.'

FITTING_AND_PREDICTING_MODELS = 'Fitting and predicting {n_models} response variables.'

FITTING_MODEL = 'Fitting model for {model_name}.'

FITTING_MODELS = 'Fitting models on {n_models} response variables.'

GENERATING_MASK_AUTOMATICALLY = 'Generating mask automatically ...'

HARMONIZING_DATA = 'Harmonizing data on {n_models} response variables.'

HARMONIZING_DATA_MODEL = 'Harmonizing data for {model_name}.'

JOB_STATUS_LINE = '{:<11} {:<9} {:<10} {:<9} {:<14}'

JOB_STATUS_MONITOR = Multiline-String

Show Value

"""
---------------------------------------------------------
              PCNtoolkit Job Status Monitor ®
---------------------------------------------------------
Task ID: {task_id}
---------------------------------------------------------
Job ID      Name          State      Time      Nodes
---------------------------------------------------------
"""

JOB_STATUS_SUMMARY = Multiline-String

Show Value

"""
---------------------------------------------------------
Total active jobs: {total_active_jobs}
Total completed jobs: {total_completed_jobs}
Total failed jobs: {total_failed_jobs}
---------------------------------------------------------
"""

LOADING_CALLABLE = 'Loading callable from {path}.'

LOADING_DATA = 'Loading data from {path}.'

LOADING_DATA_UNDER_KFOLD_CV = 'Automatically loading data under KFold CV is not implemented yet. Please load the data using...

LOADING_ROI_MASK = 'Loading ROI mask ...'

LOADING_RUNNER_STATE = Multiline-String

Show Value

"""Loading runner state from:
       {runner_file}"""

LOG_DIR_CREATED = Multiline-String

Show Value

"""Log directory created:
       {log_dir}"""

NORMATIVE_MODEL_CONFIGURATION_VALID = 'Configuration of normative model is valid.'

NO_LOG_DIR_SPECIFIED = 'No log directory specified. Using default log directory: {log_dir}'

NO_MORE_RUNNING_JOBS = Multiline-String

Show Value

"""
---------------------------------------------------------
No more running jobs!
---------------------------------------------------------
"""

NO_PYTHON_PATH_SPECIFIED = 'No python path specified. Using interpreter path of current process: {python_path}'

NO_TEMP_DIR_SPECIFIED = 'No temporary directory specified. Using default temporary directory: {temp_dir}'

PREDICTING_MODEL = 'Making predictions on {model_name}.'

PREDICTING_MODELS = 'Making predictions on {n_models} response variables.'

REGRESSION_MODEL_CONFIGURATION_VALID = 'Configuration of regression model is valid.'

RUNNER_LOADED = Multiline-String

Show Value

"""Runner loaded
---------------------------------------------------------Active jobs: {n_active_jobs}
Finished jobs: {n_finished_jobs}
Failed jobs: {n_failed_jobs}
---------------------------------------------------------"""

SAVING_CENTILES = Multiline-String

Show Value

"""Saving centiles to:
       {save_dir}."""

SAVING_MODEL = Multiline-String

Show Value

"""Saving model to:
       {save_dir}."""

SAVING_RESULTS = Multiline-String

Show Value

"""Saving results to:
       {save_dir}."""

SAVING_RUNNER_STATE = Multiline-String

Show Value

"""Saving runner state to:
       {runner_file}"""

SAVING_STATISTICS = Multiline-String

Show Value

"""Saving statistics to:
       {save_dir}."""

SAVING_ZSCORES = Multiline-String

Show Value

"""Saving z-scores to:
       {save_dir}."""

SYNTHESIZING_DATA = 'Synthesizing data for {n_models} response variables.'

SYNTHESIZING_DATA_MODEL = 'Synthesizing data for {model_name}.'

TASK_ID_CREATED = 'Task ID created: {task_id}'

TEMP_DIR_CREATED = Multiline-String

Show Value

"""Temporary directory created:
       {temp_dir}"""

TRANSFERRING_MODEL = 'Transferring model for {model_name}.'

TRANSFERRING_MODELS = 'Transferring models on {n_models} response variables.'

class Output

classmethod error(message: str, *args, **kwargs) → str

Print error message

classmethod get_show_messages() → bool

classmethod get_show_pid() → bool

classmethod get_show_timestamp() → bool

classmethod get_show_warnings() → bool

classmethod print(message: str, *args, **kwargs) → None

Print message only if show_messages mode is enabled

classmethod set_show_messages(value: bool) → None

classmethod set_show_pid(value: bool) → None

classmethod set_show_timestamp(value: bool) → None

classmethod set_show_warnings(value: bool) → None

classmethod warning(message: str, *args, category: type = UserWarning, **kwargs) → None

Print warning only if show_warnings mode is enabled.

class Warnings

BATCH_SIZE_AND_N_BATCHES_SPECIFIED = 'Batch size and number of batches specified. Batch size will be ignored.'

BLR_BATCH_EFFECTS_NOT_PROVIDED = 'batch_effects is not provided, setting self.batch_effects to zeros'

BLR_CG_NOT_SUPPORTED_WITH_HETEROSKEDASTIC = "The 'cg' optimizer requires analytical gradients, which are not implemented for heteroskedastic...

BLR_CG_NOT_SUPPORTED_WITH_WARP = "The 'cg' optimizer requires analytical gradients, which are not implemented for warped models....

BLR_ESTIMATION_OF_POSTERIOR_DISTRIBUTION_FAILED = Multiline-String

Show Value

"""Posterior estimation failed:
{error}.
The optimizer could not find a stable solution. Retrying optimization."""

BLR_VAR_X_NOT_PROVIDED = 'var_X is not provided, setting self.var_X to zeros'

BLR_Y_NOT_PROVIDED = 'y is not provided, setting self.y to zeros'

CENTILES_ALREADY_COMPUTED_FOR_CENTILES = 'Centiles are already computed for {dataset_name} for centiles {centiles}, skipping computation....

DATA_ALREADY_SCALED = 'Data is already scaled, skipping scaling back to original scale.'

DATA_NOT_SCALED = 'Data is not scaled, skipping scaling back to original scale.'

DIR_DOES_NOT_EXIST = '{dir_attr_str} ({dir_attr}) does not exist, creating it for you.'

ERROR_GETTING_JOB_STATUSES = 'Error getting job statuses: {stderr}'

ERROR_PARSING_JOB_STATUS_LINE = 'Error parsing job status line: {line} - {error}'

ERROR_SUBMITTING_JOB = 'Error submitting job {job_id}: {stderr}'

EXTRA_COVARIATES = 'The dataset {dataset_name} has too many covariates: {covariates}'

EXTRA_RESPONSE_VARS = 'The dataset {dataset_name} has too many response variables: {response_vars}'

HBR_BATCH_EFFECTS_NOT_PROVIDED = 'batch_effects is not provided, setting self.batch_effects to zeros'

LOADING_DATA_NOT_SUPPORTED_FOR_CROSS_VALIDATION = 'Automatic data loading by the Runner is not supported for cross-validation.'

LOAD_CIFTI_GENERIC_EXCEPTION = 'A general exception occurred while loading CIFTI file: {}'

LOAD_NIFTI_GENERIC_EXCEPTION = 'A general exception occurred while loading NIFTI file: {}'

MISSING_COVARIATES = 'The dataset {dataset_name} is missing the following covariates: {covariates}'

MODEL_MIGRATION_APPLIED = 'This model was saved with PCNtoolkit v{saved_version}, but you are running v{current_version}....

MODEL_SAVED_WITH_NEWER_VERSION = 'This model was saved with PCNtoolkit v{saved_version}, but you are running v{current_version}....

MULTIPLE_BATCH_EFFECT_SUMMARY = "Multiple batch effect dimensions found. The summary printout currently uses the first dimension...

MULTIPLE_JOBS_FOUND_FOR_JOB_ID = 'Multiple jobs found for job ID {job_id}: {job_name}. Please check the job statuses and try again.'

NO_COVARIATES = 'No covariates provided for dataset {dataset_name}.'

NO_RESPONSE_VARS = 'No response variables provided for dataset {dataset_name}. Please provide a list of response...

PREDICT_DATA_NOT_USED_IN_KFOLD_CROSS_VALIDATION = 'Predict data not used in k-fold cross-validation'

REMOVE_NAN_SET_TO_FALSE = 'Warning: remove_NAN is set to False. Missing (NaN) values may cause errors during model...

RENAMED = "'{old_name}' has been renamed to '{new_name}'."

RESPONSE_VAR_NOT_FOUND = 'Response variable {response_var} not found in dataset {dataset_name}. Setting to NaN.'

SUBJECT_ID_MULTIPLE_COLUMNS = 'Subject ID file contains multiple columns. Using the first column for subject IDs.'

SUBJECT_ID_UNEXPECTED_SHAPE = 'Subject ID data has an unexpected shape. Expected 1D array or 2D array with one column. Using...

SYNTHESIZE_N_SAMPLES_IGNORED = '{n_samples} sample(s) ignored because data is provided.'

THRIVELINES_ALREADY_COMPUTED_FOR = 'Thrivelines are already computed for {dataset_name} for offsets {offsets}, skipping...

TOO_FEW_OBSERVATIONS = 'Cannot compute {statistic}: {n_valid} valid observation(s) found after removing NaN/Inf values,...

TRANSFER_DATA_FEWER_BATCH_EFFECTS = 'Transfer data contain fewer batch effect levels than training data. This may lead to biased results.'

UNKNOWN_BATCH_EFFECTS = 'The dataset {dataset_name} has unknown batch effects: {batch_effects}'