Skip to content

Commit

Permalink
Minor changes (#30)
Browse files Browse the repository at this point in the history 
Minor changes to update doc-string styles
Resolve a few warnings
  • Loading branch information
@eyurtsev
eyurtsev authored Jan 24, 2021
1 parent 8d39411 commit 6229b55
Show file tree
Hide file tree
Showing 2 changed files with 43 additions and 58 deletions.
97 changes: 42 additions & 55 deletions FlowCytometryTools/core/bases.py
View file
Original file line number Diff line number Diff line change
@@ -1,17 +1,4 @@
'''
Created on Jun 18, 2013
@author: jonathanfriedman
Base objects for measurement and plate objects.
TODO:
- make plate a subclass of collection
- consider converting init methods to accepting data, and adding
factory methods for construction from files.
- consider always reading in data in measurements, perhaps storing on disk
using shelve|PyTables|pandas HDFStore
'''
"""Base objects for measurement and plate objects."""
import inspect
import os

Expand Down Expand Up @@ -83,7 +70,7 @@ def int2letters(x, alphabet):
"""
base = len(alphabet)
if x < 0:
raise ValueError('Only non-negative numbers are supported. Encounterd %s' % x)
raise ValueError('Only non-negative numbers are supported. Encountered %s' % x)
letters = []
quotient = x
while quotient >= 0:
Expand Down Expand Up @@ -121,10 +108,10 @@ def queueable(fun, *args, **kwargs):


class BaseObject(object):
'''
"""
Object providing common utility methods.
Used for inheritance.
'''
"""

def __repr__(self):
return '<{0} {1}>'.format(type(self).__name__, repr(self.ID))
Expand Down Expand Up @@ -163,10 +150,10 @@ def copy(self, deep=True):


class Measurement(BaseObject):
'''
"""
A class for holding data from a single measurement, i.e.
a single well or a single tube.
'''
"""

def __init__(self, ID,
datafile=None, readdata=False, readdata_kwargs={},
Expand Down Expand Up @@ -230,41 +217,41 @@ def __getitem__(self, key):
# Methods getting/setting data
# ----------------------
def read_data(self, **kwargs):
'''
"""
This function should be overwritten for each
specific data type.
'''
"""
pass

def read_meta(self, **kwargs):
'''
"""
This function should be overwritten for each
specific data type.
'''
"""
pass

def set_data(self, data=None, **kwargs):
'''
"""
Read data into memory, applying all actions in queue.
Additionally, update queue and history.
'''
"""
if data is None:
data = self.get_data(**kwargs)
setattr(self, '_data', data)
self.history += self.queue
self.queue = []

def set_meta(self, meta=None, **kwargs):
'''
"""
Assign values to self.meta.
Meta is not returned
'''
"""
if meta is None:
meta = self.get_meta(**kwargs)
setattr(self, '_meta', meta)

def _get_attr_from_file(self, name, **kwargs):
'''
"""
return values of attribute of self.
Attribute values can the ones assigned already, or the read for
the corresponding file.
Expand All @@ -275,7 +262,7 @@ def _get_attr_from_file(self, name, **kwargs):
ii) the file path will be the one specified in an attribute
named: '[attr name]file'. (e.g. for an attribute named
'meta' a 'metafile' attribute will be created).
'''
"""
current_value = getattr(self, '_' + name)
if current_value is not None:
value = current_value
Expand All @@ -285,43 +272,43 @@ def _get_attr_from_file(self, name, **kwargs):
return value

def get_data(self, **kwargs):
'''
"""
Get the measurement data.
If data is not set, read from 'self.datafile' using 'self.read_data'.
'''
"""
if self.queue:
new = self.apply_queued()
return new.get_data()
else:
return self._get_attr_from_file('data', **kwargs)

def get_meta(self, **kwargs):
'''
"""
Get the measurement metadata.
If not metadata is not set, read from 'self.metafile' using 'self.read_meta'.
'''
"""
return self._get_attr_from_file('meta', **kwargs)

data = property(get_data, set_data, doc='Data may be stored in memory or on disk')
meta = property(get_meta, set_meta, doc='Metadata associated with measurement.')

# ----------------------
def get_meta_fields(self, fields, **kwargs):
'''
"""
Get specific fields of associated metadata.
This function should be overwritten for each
specific data type.
'''
"""
pass

def ID_from_data(self):
'''
"""
Get measurement ID from loaded data.
This function should be overwritten for each
specific data type.
'''
"""
pass

def apply(self, func, applyto='measurement', noneval=nan, setdata=False):
Expand Down Expand Up @@ -367,13 +354,13 @@ def apply(self, func, applyto='measurement', noneval=nan, setdata=False):


class MeasurementCollection(collections.MutableMapping, BaseObject):
'''
"""
A collection of measurements
'''
"""
_measurement_class = Measurement # to be replaced when inheriting

def __init__(self, ID, measurements):
'''
"""
A dictionary-like container for holding multiple Measurements.
Note that the collection keys are not necessarily identical to the Measurements IDs.
Expand All @@ -385,7 +372,7 @@ def __init__(self, ID, measurements):
Collection ID
measurements : mappable | iterable
values are measurements of appropriate type (type is explicitly check for).
'''
"""
self.ID = ID
self.data = {}
if isinstance(measurements, collections.Mapping):
Expand Down Expand Up @@ -476,7 +463,7 @@ def __len__(self):
def apply(self, func, ids=None, applyto='measurement', noneval=nan,
setdata=False, output_format='dict', ID=None,
**kwargs):
'''
"""
Apply func to each of the specified measurements.
Parameters
Expand All @@ -502,7 +489,7 @@ def apply(self, func, ids=None, applyto='measurement', noneval=nan,
-------
Dictionary keyed by measurement keys containing the corresponding output of func
or returns a collection (if output_format='collection').
'''
"""
if ids is None:
ids = self.keys()
else:
Expand Down Expand Up @@ -812,10 +799,10 @@ def from_dir(cls, ID, path,
ID_kwargs=ID_kwargs, **kwargs)

def set_labels(self, labels, axis='rows'):
'''
"""
Set the row/col labels.
Note that this method doesn't check that enough labels were set for all the assigned positions.
'''
"""
if axis.lower() in ('rows', 'row', 'r', 0):
assigned_pos = set(v[0] for v in self._positions.itervalues())
not_assigned = set(labels) - assigned_pos
Expand All @@ -836,17 +823,17 @@ def _default_labels(self, axis, shape):
return range(1, 1 + shape[1])

def _is_valid_position(self, position):
'''
"""
check if given position is valid for this collection
'''
"""
row, col = position
valid_r = row in self.row_labels
valid_c = col in self.col_labels
return valid_r and valid_c

@doc_replacer
def _get_ID2position_mapper(self, position_mapper):
'''
"""
Defines a position parser that is used
to map between sample IDs and positions.
Expand All @@ -856,7 +843,7 @@ def _get_ID2position_mapper(self, position_mapper):
TODO: Fix the name to work with more than 26 letters
of the alphabet.
'''
"""

def num_parser(x, order):
i, j = unravel_index(int(x - 1), self.shape, order=order)
Expand All @@ -878,7 +865,7 @@ def num_parser(x, order):
return mapper

def set_positions(self, positions=None, position_mapper='name', ids=None):
'''
"""
checks for position validity & collisions,
but not that all measurements are assigned.
Expand All @@ -895,7 +882,7 @@ def set_positions(self, positions=None, position_mapper='name', ids=None):
If None is given, parser will be applied to all measurements.
TODO: output a more informative message for position collisions
'''
"""
if positions is None:
if ids is None:
ids = self.keys()
Expand All @@ -920,9 +907,9 @@ def set_positions(self, positions=None, position_mapper='name', ids=None):
self[k]._set_position(self.ID, pos)

def get_positions(self, copy=True):
'''
"""
Get a dictionary of measurement positions.
'''
"""
if copy:
return self._positions.copy()
else:
Expand All @@ -943,10 +930,10 @@ def _dict2DF(self, d, noneval, dropna=False):
return df

def dropna(self):
'''
"""
Remove rows and cols that have no assigned measurements.
Return new instance.
'''
"""
new = self.copy()
tmp = self._dict2DF(self, nan, True)
new.row_labels = list(tmp.index)
Expand Down
4 changes: 1 addition & 3 deletions FlowCytometryTools/core/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def get_tag_value(string, pre, post, tagtype=float, greedy=True):
the type to which the tag value should be converted to
greedy : bool
Whether the regular expression is gredy or not.
Whether the regular expression is greedy or not.
Returns
---------------
Expand All @@ -46,8 +46,6 @@ def get_tag_value(string, pre, post, tagtype=float, greedy=True):
get_tag_value('PID_23_5_.txt', pre=r'PID_', post='(?=_|\.txt)') should return 23
get_tag_value('PID_23.txt', pre=r'PID_', post='.txt') should return 23
get_tag_value('PID.txt', pre=r'PID_', post='.txt') should return None
TODO Make list/tuple input for pre
"""
greedy = '?' if greedy else '' # For greedy search

Expand Down

0 comments on commit 6229b55

Please sign in to comment.