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[ENH] Simplified saving kwargs #200

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[ENH] Simplified saving kwargs #200

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1287858
removed file_path and save_fig
ryanhammonds Mar 8, 2021
69ed1c8
io tests updated
ryanhammonds Mar 8, 2021
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72 changes: 17 additions & 55 deletions fooof/core/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,46 +33,15 @@ def fname(file_name, extension):
return file_name


def fpath(file_path, file_name):
"""Build the full file path from file name and directory.

Parameters
----------
file_path : str or None
Path to the directory where the file is located.
file_name : str
Name of the file.

Returns
-------
full_path : str
Full file path to the file, including directory, if provided.

Notes
-----
This function is mainly used to deal with the case in which file_path is None.
"""

if not file_path:
full_path = file_name
else:
full_path = os.path.join(file_path, file_name)

return full_path


def save_fm(fm, file_name, file_path=None, append=False,
save_results=False, save_settings=False, save_data=False):
def save_fm(fm, file_name, append=False, save_results=False, save_settings=False, save_data=False):
"""Save out data, results and/or settings from a FOOOF object into a JSON file.

Parameters
----------
fm : FOOOF
Object to save data from.
file_name : str or FileObject
File to save data to.
file_path : str, optional
Path to directory to save to. If None, saves to current directory.
File to save data to. Absolute or relative paths may be included.
append : bool, optional, default: False
Whether to append to an existing file, if available.
This option is only valid (and only used) if 'file_name' is a str.
Expand Down Expand Up @@ -101,12 +70,12 @@ def save_fm(fm, file_name, file_path=None, append=False,

# Save out - create new file, (creates a JSON file)
if isinstance(file_name, str) and not append:
with open(fpath(file_path, fname(file_name, 'json')), 'w') as outfile:
with open(fname(file_name, 'json'), 'w') as outfile:
json.dump(obj_dict, outfile)

# Save out - append to file_name (appends to a JSONlines file)
elif isinstance(file_name, str) and append:
with open(fpath(file_path, fname(file_name, 'json')), 'a') as outfile:
with open(fname(file_name, 'json'), 'a') as outfile:
json.dump(obj_dict, outfile)
outfile.write('\n')

Expand All @@ -119,18 +88,15 @@ def save_fm(fm, file_name, file_path=None, append=False,
raise ValueError("Save file not understood.")


def save_fg(fg, file_name, file_path=None, append=False,
save_results=False, save_settings=False, save_data=False):
def save_fg(fg, file_name, append=False, save_results=False, save_settings=False, save_data=False):
"""Save out results and/or settings from FOOOFGroup object. Saves out to a JSON file.

Parameters
----------
fg : FOOOFGroup
Object to save data from.
file_name : str or FileObject
File to save data to.
file_path : str, optional
Path to directory to load from. If None, loads from current directory.
File to save data to, including absolute or relative path.
append : bool, optional, default: False
Whether to append to an existing file, if available.
This option is only valid (and only used) if 'file_name' is a str.
Expand All @@ -152,12 +118,12 @@ def save_fg(fg, file_name, file_path=None, append=False,

# Save to string specified file, do not append
if isinstance(file_name, str) and not append:
with open(fpath(file_path, fname(file_name, 'json')), 'w') as f_obj:
with open(fname(file_name, 'json'), 'w') as f_obj:
_save_fg(fg, f_obj, save_results, save_settings, save_data)

# Save to string specified file, appending
elif isinstance(file_name, str) and append:
with open(fpath(file_path, fname(file_name, 'json')), 'a') as f_obj:
with open(fname(file_name, 'json'), 'a') as f_obj:
_save_fg(fg, f_obj, save_results, save_settings, save_data)

# Save to file-object specified file
Expand All @@ -168,15 +134,13 @@ def save_fg(fg, file_name, file_path=None, append=False,
raise ValueError("Save file not understood.")


def load_json(file_name, file_path):
def load_json(file_name):
"""Load json file.

Parameters
----------
file_name : str or FileObject
File to load data from.
file_path : str
Path to directory to load from.
File to load data from, including absolute or relative path.

Returns
-------
Expand All @@ -186,7 +150,7 @@ def load_json(file_name, file_path):

# Load data from file
if isinstance(file_name, str):
with open(fpath(file_path, fname(file_name, 'json')), 'r') as infile:
with open(fname(file_name, 'json'), 'r') as infile:
data = json.load(infile)
elif isinstance(file_name, io.IOBase):
data = json.loads(file_name.readline())
Expand All @@ -197,29 +161,27 @@ def load_json(file_name, file_path):
return data


def load_jsonlines(file_name, file_path):
def load_jsonlines(file_name):
"""Load a json-lines file, yielding data line by line.

Parameters
----------
file_name : str
File to load data from.
file_path : str
Path to directory from load from.
File to load data from, including absolute or relative path.

Yields
------
dict
Dictionary of data loaded from file.
"""

with open(fpath(file_path, fname(file_name, 'json')), 'r') as f_obj:
with open(fname(file_name, 'json'), 'r') as f_obj:

while True:

# Load each line, as JSON file
try:
yield load_json(f_obj, '')
yield load_json(f_obj)

# Break off when get a JSON error - end of the file
except JSONDecodeError:
Expand All @@ -245,11 +207,11 @@ def _save_fg(fg, f_obj, save_results, save_settings, save_data):

# Since there is a single set of object settings, save them out once, at the top
if save_settings:
save_fm(fg, file_name=f_obj, file_path=None, append=False, save_settings=True)
save_fm(fg, file_name=f_obj, append=False, save_settings=True)

# For results & data, loop across all data and/or models, and save each out to a new line
if save_results or save_data:
for ind in range(len(fg.group_results)):
fm = fg.get_fooof(ind, regenerate=False)
save_fm(fm, file_name=f_obj, file_path=None, append=False,
save_fm(fm, file_name=f_obj, append=False,
save_results=save_results, save_data=save_data)
18 changes: 7 additions & 11 deletions fooof/core/reports.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""Generate reports from FOOOF objects."""

from fooof.core.io import fname, fpath
from fooof.core.io import fname
from fooof.core.modutils import safe_import, check_dependency
from fooof.core.strings import gen_settings_str, gen_results_fm_str, gen_results_fg_str
from fooof.plts.fg import plot_fg_ap, plot_fg_gf, plot_fg_peak_cens
Expand All @@ -22,17 +22,15 @@
###################################################################################################

@check_dependency(plt, 'matplotlib')
def save_report_fm(fm, file_name, file_path=None, plt_log=False):
def save_report_fm(fm, file_name, plt_log=False):
"""Generate and save out a PDF report for a power spectrum model fit.

Parameters
----------
fm : FOOOF
Object with results from fitting a power spectrum.
file_name : str
Name to give the saved out file.
file_path : str, optional
Path to directory to save to. If None, saves to current directory.
Name of output file to save, including absolute or relative path.
plt_log : bool, optional, default: False
Whether or not to plot the frequency axis in log space.
"""
Expand Down Expand Up @@ -62,22 +60,20 @@ def save_report_fm(fm, file_name, file_path=None, plt_log=False):
ax2.set_yticks([])

# Save out the report
plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
plt.savefig(fname(file_name, SAVE_FORMAT))
plt.close()


@check_dependency(plt, 'matplotlib')
def save_report_fg(fg, file_name, file_path=None):
def save_report_fg(fg, file_name):
"""Generate and save out a PDF report for a group of power spectrum models.

Parameters
----------
fg : FOOOFGroup
Object with results from fitting a group of power spectra.
file_name : str
Name to give the saved out file.
file_path : str, optional
Path to directory to save to. If None, saves to current directory.
Name of output file to save, including absolute or relative path.
"""

# Initialize figure
Expand Down Expand Up @@ -105,5 +101,5 @@ def save_report_fg(fg, file_name, file_path=None):
plot_fg_peak_cens(fg, ax3)

# Save out the report
plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
plt.savefig(fname(file_name, SAVE_FORMAT))
plt.close()
28 changes: 12 additions & 16 deletions fooof/objs/fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -633,38 +633,34 @@ def get_results(self):


@copy_doc_func_to_method(plot_fm)
def plot(self, plot_peaks=None, plot_aperiodic=True, plt_log=False,
add_legend=True, save_fig=False, file_name=None, file_path=None,
ax=None, plot_style=style_spectrum_plot,
data_kwargs=None, model_kwargs=None, aperiodic_kwargs=None, peak_kwargs=None):
def plot(self, plot_peaks=None, plot_aperiodic=True, plt_log=False, add_legend=True,
file_name=None, ax=None, plot_style=style_spectrum_plot, data_kwargs=None,
model_kwargs=None, aperiodic_kwargs=None, peak_kwargs=None):

plot_fm(self, plot_peaks, plot_aperiodic, plt_log, add_legend,
save_fig, file_name, file_path, ax, plot_style,
data_kwargs, model_kwargs, aperiodic_kwargs, peak_kwargs)
plot_fm(self, plot_peaks, plot_aperiodic, plt_log, add_legend, file_name, ax,
plot_style, data_kwargs, model_kwargs, aperiodic_kwargs, peak_kwargs)


@copy_doc_func_to_method(save_report_fm)
def save_report(self, file_name, file_path=None, plt_log=False):
def save_report(self, file_name, plt_log=False):

save_report_fm(self, file_name, file_path, plt_log)
save_report_fm(self, file_name, plt_log)


@copy_doc_func_to_method(save_fm)
def save(self, file_name, file_path=None, append=False,
def save(self, file_name, append=False,
save_results=False, save_settings=False, save_data=False):

save_fm(self, file_name, file_path, append, save_results, save_settings, save_data)
save_fm(self, file_name, append, save_results, save_settings, save_data)


def load(self, file_name, file_path=None, regenerate=True):
def load(self, file_name, regenerate=True):
"""Load in a FOOOF formatted JSON file to the current object.

Parameters
----------
file_name : str or FileObject
File to load data from.
file_path : str or None, optional
Path to directory to load from. If None, loads from current directory.
File to load data from, including absolute or relative path.
regenerate : bool, optional, default: True
Whether to regenerate the model fit from the loaded data, if data is available.
"""
Expand All @@ -673,7 +669,7 @@ def load(self, file_name, file_path=None, regenerate=True):
self._reset_data_results(True, True, True)

# Load JSON file, add to self and check loaded data
data = load_json(file_name, file_path)
data = load_json(file_name)
self._add_from_dict(data)
self._check_loaded_settings(data)
self._check_loaded_results(data)
Expand Down
20 changes: 9 additions & 11 deletions fooof/objs/group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -398,40 +398,38 @@ def get_params(self, name, col=None):


@copy_doc_func_to_method(plot_fg)
def plot(self, save_fig=False, file_name=None, file_path=None):
def plot(self, file_name=None):

plot_fg(self, save_fig, file_name, file_path)
plot_fg(self, file_name)


@copy_doc_func_to_method(save_report_fg)
def save_report(self, file_name, file_path=None):
def save_report(self, file_name):

save_report_fg(self, file_name, file_path)
save_report_fg(self, file_name)


@copy_doc_func_to_method(save_fg)
def save(self, file_name, file_path=None, append=False,
def save(self, file_name, append=False,
save_results=False, save_settings=False, save_data=False):

save_fg(self, file_name, file_path, append, save_results, save_settings, save_data)
save_fg(self, file_name, append, save_results, save_settings, save_data)


def load(self, file_name, file_path=None):
def load(self, file_name):
"""Load FOOOFGroup data from file.

Parameters
----------
file_name : str
File to load data from.
file_path : str, optional
Path to directory to load from. If None, loads from current directory.
File to load data from, including absolute or relative path.
"""

# Clear results so as not to have possible prior results interfere
self._reset_group_results()

power_spectra = []
for ind, data in enumerate(load_jsonlines(file_name, file_path)):
for ind, data in enumerate(load_jsonlines(file_name)):

self._add_from_dict(data)

Expand Down
18 changes: 6 additions & 12 deletions fooof/plts/fg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
This file contains plotting functions that take as input a FOOOFGroup object.
"""

from fooof.core.io import fname, fpath
from fooof.core.io import fname
from fooof.core.errors import NoModelError
from fooof.core.modutils import safe_import, check_dependency
from fooof.plts.settings import PLT_FIGSIZES
Expand All @@ -18,19 +18,15 @@
###################################################################################################

@check_dependency(plt, 'matplotlib')
def plot_fg(fg, save_fig=False, file_name=None, file_path=None):
def plot_fg(fg, file_name=None):
"""Plot a figure with subplots visualizing the parameters from a FOOOFGroup object.

Parameters
----------
fg : FOOOFGroup
Object containing results from fitting a group of power spectra.
save_fig : bool, optional, default: False
Whether to save out a copy of the plot.
file_name : str, optional
Name to give the saved out file.
file_path : str, optional
Path to directory to save to. If None, saves to current directory.
file_name : str, optional, default: None
Name with format to save as, including absolute or relative path.

Raises
------
Expand All @@ -56,10 +52,8 @@ def plot_fg(fg, save_fig=False, file_name=None, file_path=None):
ax2 = plt.subplot(gs[1, :])
plot_fg_peak_cens(fg, ax2)

if save_fig:
if not file_name:
raise ValueError("Input 'file_name' is required to save out the plot.")
plt.savefig(fpath(file_path, fname(file_name, 'png')))
if file_name is not None:
plt.savefig(fname(file_name, 'png'))


@check_dependency(plt, 'matplotlib')
Expand Down
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