Source code for

"""Experiment data storage.

There are two main use cases for the functionality in this module:
reading/writing data during an experiment session, and reading data once an
experiment is complete (i.e. for analysis). See the :ref:`user guide <storage>`
for information on these use cases/api.jpeg/api.jpeg/api.jpeg.

import os
import h5py
import numpy
import pandas
import zipfile
import shutil
import pickle
import logging

# Highest layer. Used by tasks to obtain task readers/writers

[docs]class Storage(object): """Top-level data storage maintainer. See the :ref:`user guide <storage>` for more information. Parameters ---------- root : str, optional Path to the root of the data storage filestructure. By default, 'data' is used. If the directory doesn't exist, it is created. allow_overwrite : bool, optional Specifies whether or not the storage interface allows you to overwrite a task's data for a subject if it already exists. """ def __init__(self, root='data', allow_overwrite=False): self.root = root self.allow_overwrite = allow_overwrite makedirs(root, exist_ok=True) self._subject_id = None @property def subject_ids(self): """Generate subject IDs found in storage sorted in alphabetical order. Returns ------- subject_id : str ID of the subject found. """ ls = os.listdir(self.root) for name in sorted(ls): path = os.path.join(self.root, name) if os.path.isdir(path): yield name @property def subject_id(self): """The current subject ID. When setting the subject ID for a new subject (i.e. one that doesn't exist already), storage for that subject is created. """ return self._subject_id @subject_id.setter def subject_id(self, val): makedirs(os.path.join(self.root, val), exist_ok=True) self._subject_id = val @property def task_ids(self): """Generate names of tasks found for the current subject. Note that there may be no tasks found if the `subject_id` has not been set or if the subject hasn't started any tasks. In this case, nothing is yielded. """ if self.subject_id is None: return subj_path = os.path.join(self.root, self.subject_id) ls = os.listdir(subj_path) for name in sorted(ls): path = os.path.join(subj_path, name) if os.path.isdir(path): yield name
[docs] def create_task(self, task_id): """Create a task for the current subject. Parameters ---------- task_id : str The ID of the task to add. The name must not have been used for another task for the current subject. Returns ------- writer : TaskWriter A new TaskWriter for storing task data. """ path = self._task_path(task_id) try: makedirs(path) except OSError: if self.allow_overwrite: shutil.rmtree(path) makedirs(path) else: raise ValueError( "Subject {} has already started \"{}\". Only unique task " "names are allowed.".format(self.subject_id, task_id)) return TaskWriter(path)
[docs] def require_task(self, task_id): """Retrieves a task for the current subject. Parameters ---------- task_id : str The ID of the task to look for. The task must have already been run with the current subject. Returns ------- reader : TaskReader A new TaskReader for working with the existing task data. """ if task_id not in self.task_ids: raise ValueError( "Subject {} has not started \"{}\" yet. Use `create_task` to " "create it first.".format(self.subject_id, task_id)) path = self._task_path(task_id) return TaskReader(path)
[docs] def to_zip(self, outfile): """Create a ZIP archive from a data storage hierarchy. For more information, see :func:`storage_to_zip`. """ storage_to_zip(self.root, outfile)
def _task_path(self, task_id): return os.path.join(self.root, self.subject_id, task_id)
# # Middle layer. Used by tasks to read/write data. #
[docs]class TaskWriter(object): """The main interface for storing data from a task. Usually you get a :class:`Taskwriter` from :class:`Storage`, so you don't normally need to create one yourself. Parameters ---------- root : str Path to the task root (e.g. 'data/subject_1/taskname'). Attributes ---------- trials : TrialWriter :class:`TrialWriter` for storing trial data. """ def __init__(self, root): self.root = root self.trials = TrialWriter(_trials_path(self.root))
[docs] def write(self, trial): """Write trial data. This must be the last thing done for the current trial. That is, make sure all arrays have accumulated all data required. This method flushes trial and array data to files for you. **Important note**: The trial's arrays are cleared after writing. Parameters ---------- trial : Trial Tral data. See :meth:`TrialWriter.write` and :class:`Trial` for details. """'saving trial {}:{}\n{}'.format( trial.attrs['block'], trial.attrs['trial'], str(trial))) self.trials.write(trial.attrs) ind = self.trials.df.index[-1] for name, array in trial.arrays.items(): path = _array_path(self.root, name) write_hdf5(path,, dataset=str(ind)) array.clear()
[docs] def pickle(self, obj, name): """Write a generic object to storage. This can be useful to persist an object from one task to another, or to store something that doesn't easily fit into the AxoPy storage model (trial attributes and arrays). Be cautious, however, as pickles are not the best way to store things long-term nor securely. See the advice given here, for example: Parameters ---------- obj : object The object to pickle. name : str Name of the pickle to save (no extension). """ with open(_pickle_path(self.root, name), 'wb') as f: pickle.dump(obj, f)
[docs]class TaskReader(object): """High-level interface to task storage. Parameters ---------- root : str Path to task's root directory. This is the directory specific to a task which contains a ``trials.csv`` file and HDF5 array files. """ def __init__(self, root): self.root = root self._trials = None @property def trials(self): """A Pandas DataFrame representing the trial data.""" if self._trials is None: self._trials = pandas.read_csv(_trials_path(self.root)) return self._trials
[docs] def iterarray(self, name): """Iteratively retrieve an array for each trial. Parameters ---------- name : str Name of the array type. """ for ind in self.trials.index: dset = str(ind) yield read_hdf5(_array_path(self.root, name), dataset=dset)
[docs] def array(self, name): """Retrieve an array type's data for all trials.""" return numpy.vstack(self.iterarray(name))
[docs] def pickle(self, name): """Load a pickled object from storage. Parameters ---------- name : str Name of the pickled object (no extension). """ with open(_pickle_path(self.root, name), 'rb') as f: obj = pickle.load(f) return obj
# # Lowest layer. Used by TaskReader/TaskWriter. #
[docs]class TrialWriter(object): """Writes trial data to a CSV file line by line. Parameters ---------- filepath : str Path to the file to create. Attributes ---------- data : dict Dictionary containing all trial data written so far. """ def __init__(self, filepath): self.filepath = filepath = {}
[docs] def write(self, data): """Add a single row to the trials dataset. Data is immediately added to the file on disk. Parameters ---------- data : dict Data values to add. """ for col, val in data.items(): if col not in[col] = [][col].append(val) self.df = pandas.DataFrame( self.df.to_csv(self.filepath, index=False)
# # Utilities # def _trials_path(taskroot): return os.path.join(taskroot, 'trials.csv') def _array_path(taskroot, arrayname): return os.path.join(taskroot, '{}.hdf5'.format(arrayname)) def _pickle_path(taskroot, picklename): return os.path.join(taskroot, '{}.pkl'.format(picklename))
[docs]def read_hdf5(filepath, dataset='data'): """Read the contents of a dataset. This function assumes the dataset in the HDF5 file exists at the root of the file (i.e. at '/'). It is primarily for internal usage but you may find it useful for quickly grabbing an array from an HDF5 file. Parameters ---------- filepath : str Path to the file to read from. dataset : str, optional Name of the dataset to retrieve. By default, 'data' is used. Returns ------- data : ndarray The data (read into memory) as a NumPy array. The dtype, shape, etc. is all determined by whatever is in the file. """ with h5py.File(filepath, 'r') as f: return f.get('/{}'.format(dataset))[:]
[docs]def write_hdf5(filepath, data, dataset='data'): """Write data to an hdf5 file. The data is written to a new file with a single dataset called "data" in the root group. It is primarily for internal usage but you may find it useful for quickly writing an array to an HDF5 file. Parameters ---------- filepath : str Path to the file to be written. data : ndarray NumPy array containing the data to write. The dtype, shape, etc. of the resulting dataset in storage is determined by this array directly. dataset : str, optional Name of the dataset to create. Default is 'data'. """ with h5py.File(filepath, 'a') as f: f.create_dataset(dataset, data=data)
[docs]def storage_to_zip(path, outfile=None): """Create a ZIP archive from a data storage hierarchy. The contents of the data storage hierarchy are all placed in the archive, with the top-level folder in the archive being the data storage root folder itself. That is, all paths within the ZIP file are relative to the dataset root folder. Parameters ---------- path : str Path to the root of the dataset. outfile : str, optional Name of the ZIP file to create. If not specified, the file is created in the same directory as the data root with the same name as the dataset root directory (with ".zip" added). Returns ------- outfile : str The name of the ZIP file created. """ datapath, datadir = os.path.split(path) if outfile is None: # absolute path to parent of data root + dataset name + .zip outfile = os.path.join(datapath, datadir + '.zip') with zipfile.ZipFile(outfile, 'w') as zipf: for root, dirs, files in os.walk(path): for f in files: # write as *relative* path from data root zipf.write(os.path.join(root, f), arcname=os.path.join(datadir, f)) return outfile
[docs]def makedirs(path, exist_ok=False): """Recursively create directories. This is needed for Python versions earlier than 3.2, otherwise ``os.makedirs(path, exist_ok=True)`` would suffice. Parameters ---------- path : str Path to directory to create. exist_ok : bool, optional If `exist_ok` is False (default), an exception is raised. Set to True if it is acceptable that the directory already exists. """ try: os.makedirs(path) except OSError: if not exist_ok: raise