From 1287858d98fe95049996803bb95cf0de32db21cc Mon Sep 17 00:00:00 2001 From: ryanhammonds Date: Mon, 8 Mar 2021 14:05:38 -0800 Subject: [PATCH 1/2] removed file_path and save_fig --- fooof/core/io.py | 72 ++++++++++--------------------------------- fooof/core/reports.py | 18 +++++------ fooof/objs/fit.py | 28 ++++++++--------- fooof/objs/group.py | 20 ++++++------ fooof/plts/fg.py | 18 ++++------- fooof/plts/fm.py | 21 +++++-------- fooof/utils/io.py | 16 ++++------ 7 files changed, 64 insertions(+), 129 deletions(-) diff --git a/fooof/core/io.py b/fooof/core/io.py index 037238ae1..d7a5e5713 100644 --- a/fooof/core/io.py +++ b/fooof/core/io.py @@ -33,36 +33,7 @@ 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 @@ -70,9 +41,7 @@ def save_fm(fm, file_name, file_path=None, append=False, 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. @@ -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') @@ -119,8 +88,7 @@ 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 @@ -128,9 +96,7 @@ def save_fg(fg, file_name, file_path=None, append=False, 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. @@ -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 @@ -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 ------- @@ -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()) @@ -197,15 +161,13 @@ 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 ------ @@ -213,13 +175,13 @@ def load_jsonlines(file_name, file_path): 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: @@ -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) diff --git a/fooof/core/reports.py b/fooof/core/reports.py index 20323b1ce..9842d3226 100644 --- a/fooof/core/reports.py +++ b/fooof/core/reports.py @@ -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 @@ -22,7 +22,7 @@ ################################################################################################### @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 @@ -30,9 +30,7 @@ def save_report_fm(fm, file_name, file_path=None, plt_log=False): 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. """ @@ -62,12 +60,12 @@ 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 @@ -75,9 +73,7 @@ def save_report_fg(fg, file_name, file_path=None): 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 @@ -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() diff --git a/fooof/objs/fit.py b/fooof/objs/fit.py index fba745d27..f92f5136f 100644 --- a/fooof/objs/fit.py +++ b/fooof/objs/fit.py @@ -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. """ @@ -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) diff --git a/fooof/objs/group.py b/fooof/objs/group.py index 91abcee9e..a80687a0d 100644 --- a/fooof/objs/group.py +++ b/fooof/objs/group.py @@ -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) diff --git a/fooof/plts/fg.py b/fooof/plts/fg.py index f4d121419..928c2d215 100644 --- a/fooof/plts/fg.py +++ b/fooof/plts/fg.py @@ -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 @@ -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 ------ @@ -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') diff --git a/fooof/plts/fm.py b/fooof/plts/fm.py index 68be6ea5b..2e262c611 100644 --- a/fooof/plts/fm.py +++ b/fooof/plts/fm.py @@ -7,7 +7,7 @@ import numpy as np -from fooof.core.io import fname, fpath +from fooof.core.io import fname from fooof.core.utils import nearest_ind from fooof.core.modutils import safe_import, check_dependency from fooof.sim.gen import gen_periodic @@ -25,8 +25,7 @@ @check_dependency(plt, 'matplotlib') def plot_fm(fm, 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, + file_name=None, ax=None, plot_style=style_spectrum_plot, data_kwargs=None, model_kwargs=None, aperiodic_kwargs=None, peak_kwargs=None): """Plot the power spectrum and model fit results from a FOOOF object. @@ -43,13 +42,9 @@ def plot_fm(fm, plot_peaks=None, plot_aperiodic=True, plt_log=False, add_legend= Whether to plot the frequency values in log10 spacing. add_legend : boolean, optional, default: False Whether to add a legend describing the plot components. - 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. - ax : matplotlib.Axes, optional + file_name : str, optional, default: None + Name with format to save as, including absolute or relative path. + ax : matplotlib.Axes, optional, default: None Figure axes upon which to plot. plot_style : callable, optional, default: style_spectrum_plot A function to call to apply styling & aesthetics to the plot. @@ -100,10 +95,8 @@ def plot_fm(fm, plot_peaks=None, plot_aperiodic=True, plt_log=False, add_legend= check_n_style(plot_style, ax, log_freqs, True) # Save out figure, if requested - 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')) def _add_peaks(fm, approach, plt_log, ax, peak_kwargs): diff --git a/fooof/utils/io.py b/fooof/utils/io.py index 3c2449a46..0a4b0e465 100644 --- a/fooof/utils/io.py +++ b/fooof/utils/io.py @@ -3,15 +3,13 @@ ################################################################################################### ################################################################################################### -def load_fooof(file_name, file_path=None, regenerate=True): +def load_fooof(file_name, regenerate=True): """Load a FOOOF file into a FOOOF object. Parameters ---------- file_name : str or FileObject - File to load the data from. - file_path : str or None, optional - Path to directory to load from. If None, loads from current directory. + File to load the 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. @@ -26,20 +24,18 @@ def load_fooof(file_name, file_path=None, regenerate=True): fm = FOOOF() # Load data into object - fm.load(file_name, file_path, regenerate) + fm.load(file_name, regenerate) return fm -def load_fooofgroup(file_name, file_path=None): +def load_fooofgroup(file_name): """Load data from file into a FOOOFGroup object. Parameters ---------- file_name : str - File to load data data. - file_path : str, optional - Path to directory to load from. If None, loads from current directory. + File to load data data, including absolute or relative path. Returns ------- @@ -52,6 +48,6 @@ def load_fooofgroup(file_name, file_path=None): fg = FOOOFGroup() # Load data into object - fg.load(file_name, file_path) + fg.load(file_name) return fg From 69ed1c8e253bc0e76642cbfb022da233799fd8bc Mon Sep 17 00:00:00 2001 From: ryanhammonds Date: Mon, 8 Mar 2021 14:05:54 -0800 Subject: [PATCH 2/2] io tests updated --- fooof/tests/core/test_io.py | 91 +++++++++++++++----------------- fooof/tests/core/test_reports.py | 10 ++-- fooof/tests/objs/test_fit.py | 17 +++--- fooof/tests/objs/test_group.py | 17 +++--- fooof/tests/utils/test_io.py | 9 ++-- 5 files changed, 71 insertions(+), 73 deletions(-) diff --git a/fooof/tests/core/test_io.py b/fooof/tests/core/test_io.py index adbf4f9b3..de3bff449 100644 --- a/fooof/tests/core/test_io.py +++ b/fooof/tests/core/test_io.py @@ -21,43 +21,38 @@ def test_fname(): assert fname('report.pdf', 'pdf') == 'report.pdf' assert fname('report.png', 'pdf') == 'report.png' -def test_fpath(): - """Check that the file path checker helper function properly checks / combines file paths.""" - - assert fpath(None, 'data.json') == 'data.json' - assert fpath('/path/', 'data.json') == '/path/data.json' def test_save_fm_str(tfm): """Check saving fm data, with file specifiers as strings.""" # Test saving out each set of save elements - file_name_res = 'test_fooof_res' - file_name_set = 'test_fooof_set' - file_name_dat = 'test_fooof_dat' + file_name_res = os.path.join(TEST_DATA_PATH, 'test_fooof_res') + file_name_set = os.path.join(TEST_DATA_PATH,'test_fooof_set') + file_name_dat = os.path.join(TEST_DATA_PATH,'test_fooof_dat') - save_fm(tfm, file_name_res, TEST_DATA_PATH, False, True, False, False) - save_fm(tfm, file_name_set, TEST_DATA_PATH, False, False, True, False) - save_fm(tfm, file_name_dat, TEST_DATA_PATH, False, False, False, True) + save_fm(tfm, file_name_res, False, True, False, False) + save_fm(tfm, file_name_set, False, False, True, False) + save_fm(tfm, file_name_dat, False, False, False, True) - assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_res + '.json')) - assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_set + '.json')) - assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_dat + '.json')) + assert os.path.exists(file_name_res + '.json') + assert os.path.exists(file_name_set + '.json') + assert os.path.exists(file_name_dat + '.json') # Test saving out all save elements - file_name_all = 'test_fooof_all' - save_fm(tfm, file_name_all, TEST_DATA_PATH, False, True, True, True) - assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_all + '.json')) + file_name_all = os.path.join(TEST_DATA_PATH, 'test_fooof_all') + save_fm(tfm, file_name_all, False, True, True, True) + assert os.path.exists(file_name_all + '.json') def test_save_fm_append(tfm): """Check saving fm data, appending to a file.""" - file_name = 'test_fooof_append' + file_name = os.path.join(TEST_DATA_PATH, 'test_fooof_append') - save_fm(tfm, file_name, TEST_DATA_PATH, True, True, True, True) - save_fm(tfm, file_name, TEST_DATA_PATH, True, True, True, True) + save_fm(tfm, file_name, True, True, True, True) + save_fm(tfm, file_name, True, True, True, True) - assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json')) + assert os.path.exists(file_name + '.json') def test_save_fm_fobj(tfm): """Check saving fm data, with file object file specifier.""" @@ -66,41 +61,41 @@ def test_save_fm_fobj(tfm): # Save, using file-object: three successive lines with three possible save settings with open(os.path.join(TEST_DATA_PATH, file_name + '.json'), 'w') as f_obj: - save_fm(tfm, f_obj, TEST_DATA_PATH, False, True, False, False) - save_fm(tfm, f_obj, TEST_DATA_PATH, False, False, True, False) - save_fm(tfm, f_obj, TEST_DATA_PATH, False, False, False, True) + save_fm(tfm, f_obj, False, True, False, False) + save_fm(tfm, f_obj, False, False, True, False) + save_fm(tfm, f_obj, False, False, False, True) assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json')) def test_save_fg(tfg): """Check saving fg data.""" - res_file_name = 'test_fooofgroup_res' - set_file_name = 'test_fooofgroup_set' - dat_file_name = 'test_fooofgroup_dat' + res_file_name = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_res') + set_file_name = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_set') + dat_file_name = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_dat') - save_fg(tfg, file_name=res_file_name, file_path=TEST_DATA_PATH, save_results=True) - save_fg(tfg, file_name=set_file_name, file_path=TEST_DATA_PATH, save_settings=True) - save_fg(tfg, file_name=dat_file_name, file_path=TEST_DATA_PATH, save_data=True) + save_fg(tfg, file_name=res_file_name, save_results=True) + save_fg(tfg, file_name=set_file_name, save_settings=True) + save_fg(tfg, file_name=dat_file_name, save_data=True) - assert os.path.exists(os.path.join(TEST_DATA_PATH, res_file_name + '.json')) - assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json')) - assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '.json')) + assert os.path.exists(res_file_name + '.json') + assert os.path.exists(set_file_name + '.json') + assert os.path.exists(dat_file_name + '.json') # Test saving out all save elements file_name_all = 'test_fooofgroup_all' - save_fg(tfg, file_name_all, TEST_DATA_PATH, False, True, True, True) + save_fg(tfg, os.path.join(TEST_DATA_PATH, file_name_all), False, True, True, True) assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_all + '.json')) def test_save_fg_append(tfg): """Check saving fg data, appending to file.""" - file_name = 'test_fooofgroup_append' + file_name = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_append') - save_fg(tfg, file_name, TEST_DATA_PATH, True, save_results=True) - save_fg(tfg, file_name, TEST_DATA_PATH, True, save_results=True) + save_fg(tfg, file_name, True, save_results=True) + save_fg(tfg, file_name, True, save_results=True) - assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json')) + assert os.path.exists(file_name + '.json') def test_save_fg_fobj(tfg): """Check saving fg data, with file object file specifier.""" @@ -108,7 +103,7 @@ def test_save_fg_fobj(tfg): file_name = 'test_fooof_fileobj' with open(os.path.join(TEST_DATA_PATH, file_name + '.json'), 'w') as f_obj: - save_fg(tfg, f_obj, TEST_DATA_PATH, False, True, False, False) + save_fg(tfg, f_obj, False, True, False, False) assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json')) @@ -117,9 +112,9 @@ def test_load_json_str(): Loads files from test_save_fm_str. """ - file_name = 'test_fooof_all' + file_name = os.path.join(TEST_DATA_PATH, 'test_fooof_all') - data = load_json(file_name, TEST_DATA_PATH) + data = load_json(file_name) assert data @@ -128,10 +123,10 @@ def test_load_json_fobj(): Loads files from test_save_fm_str. """ - file_name = 'test_fooof_all' + file_name = os.path.join(TEST_DATA_PATH, 'test_fooof_all') - with open(os.path.join(TEST_DATA_PATH, file_name + '.json'), 'r') as f_obj: - data = load_json(f_obj, '') + with open(file_name + '.json', 'r') as f_obj: + data = load_json(f_obj) assert data @@ -140,9 +135,9 @@ def test_load_jsonlines(): Loads files from test_save_fg. """ - res_file_name = 'test_fooofgroup_res' + res_file_name = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_res') - for data in load_jsonlines(res_file_name, TEST_DATA_PATH): + for data in load_jsonlines(res_file_name): assert data def test_load_file_contents(): @@ -150,8 +145,8 @@ def test_load_file_contents(): Note that is this test fails, it likely stems from an issue from saving. """ - file_name = 'test_fooof_all' - loaded_data = load_json(file_name, TEST_DATA_PATH) + file_name = os.path.join(TEST_DATA_PATH, 'test_fooof_all') + loaded_data = load_json(file_name) # Check settings for setting in OBJ_DESC['settings']: diff --git a/fooof/tests/core/test_reports.py b/fooof/tests/core/test_reports.py index cf6fc5ceb..507666173 100644 --- a/fooof/tests/core/test_reports.py +++ b/fooof/tests/core/test_reports.py @@ -11,16 +11,16 @@ def test_save_report_fm(tfm, skip_if_no_mpl): - file_name = 'test_report' + file_name = os.path.join(TEST_REPORTS_PATH, 'test_report') - save_report_fm(tfm, file_name, TEST_REPORTS_PATH) + save_report_fm(tfm, file_name) assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf')) def test_save_report_fg(tfg, skip_if_no_mpl): - file_name = 'test_group_report' + file_name = os.path.join(TEST_REPORTS_PATH, 'test_group_report') - save_report_fg(tfg, file_name, TEST_REPORTS_PATH) + save_report_fg(tfg, file_name) - assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf')) + assert os.path.exists(file_name + '.pdf') diff --git a/fooof/tests/objs/test_fit.py b/fooof/tests/objs/test_fit.py index 87907d11a..e26dfb562 100644 --- a/fooof/tests/objs/test_fit.py +++ b/fooof/tests/objs/test_fit.py @@ -6,6 +6,7 @@ They serve rather as 'smoke tests', for if anything fails completely. """ +import os import numpy as np from py.test import raises @@ -179,8 +180,8 @@ def test_fooof_load(): # Test loading just results tfm = FOOOF(verbose=False) - file_name_res = 'test_fooof_res' - tfm.load(file_name_res, TEST_DATA_PATH) + file_name_res = os.path.join(TEST_DATA_PATH, 'test_fooof_res') + tfm.load(file_name_res) # Check that result attributes get filled for result in OBJ_DESC['results']: assert not np.all(np.isnan(getattr(tfm, result))) @@ -193,8 +194,8 @@ def test_fooof_load(): # Test loading just settings tfm = FOOOF(verbose=False) - file_name_set = 'test_fooof_set' - tfm.load(file_name_set, TEST_DATA_PATH) + file_name_set = os.path.join(TEST_DATA_PATH, 'test_fooof_set') + tfm.load(file_name_set) for setting in OBJ_DESC['settings']: assert getattr(tfm, setting) is not None # Test that results and data are None @@ -204,8 +205,8 @@ def test_fooof_load(): # Test loading just data tfm = FOOOF(verbose=False) - file_name_dat = 'test_fooof_dat' - tfm.load(file_name_dat, TEST_DATA_PATH) + file_name_dat = os.path.join(TEST_DATA_PATH, 'test_fooof_dat') + tfm.load(file_name_dat) assert tfm.power_spectrum is not None # Test that settings and results are None for setting in OBJ_DESC['settings']: @@ -215,8 +216,8 @@ def test_fooof_load(): # Test loading all elements tfm = FOOOF(verbose=False) - file_name_all = 'test_fooof_all' - tfm.load(file_name_all, TEST_DATA_PATH) + file_name_all = os.path.join(TEST_DATA_PATH, 'test_fooof_all') + tfm.load(file_name_all) for result in OBJ_DESC['results']: assert not np.all(np.isnan(getattr(tfm, result))) for setting in OBJ_DESC['settings']: diff --git a/fooof/tests/objs/test_group.py b/fooof/tests/objs/test_group.py index 7a90cfd56..5f8962ef8 100644 --- a/fooof/tests/objs/test_group.py +++ b/fooof/tests/objs/test_group.py @@ -6,6 +6,7 @@ They serve rather as 'smoke tests', for if anything fails completely. """ +import os import numpy as np from numpy.testing import assert_equal @@ -236,13 +237,13 @@ def test_fg_plot(tfg, skip_if_no_mpl): def test_fg_load(): """Test load into FOOOFGroup. Note: loads files from test_core_io.""" - file_name_res = 'test_fooofgroup_res' - file_name_set = 'test_fooofgroup_set' - file_name_dat = 'test_fooofgroup_dat' + file_name_res = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_res') + file_name_set = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_set') + file_name_dat = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_dat') # Test loading just results tfg = FOOOFGroup(verbose=False) - tfg.load(file_name_res, TEST_DATA_PATH) + tfg.load(file_name_res) assert len(tfg.group_results) > 0 # Test that settings and data are None # Except for aperiodic mode, which can be inferred from the data @@ -253,7 +254,7 @@ def test_fg_load(): # Test loading just settings tfg = FOOOFGroup(verbose=False) - tfg.load(file_name_set, TEST_DATA_PATH) + tfg.load(file_name_set) for setting in OBJ_DESC['settings']: assert getattr(tfg, setting) is not None # Test that results and data are None @@ -263,7 +264,7 @@ def test_fg_load(): # Test loading just data tfg = FOOOFGroup(verbose=False) - tfg.load(file_name_dat, TEST_DATA_PATH) + tfg.load(file_name_dat) assert tfg.power_spectra is not None # Test that settings and results are None for setting in OBJ_DESC['settings']: @@ -273,8 +274,8 @@ def test_fg_load(): # Test loading all elements tfg = FOOOFGroup(verbose=False) - file_name_all = 'test_fooofgroup_all' - tfg.load(file_name_all, TEST_DATA_PATH) + file_name_all = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_all') + tfg.load(file_name_all) assert len(tfg.group_results) > 0 for setting in OBJ_DESC['settings']: assert getattr(tfg, setting) is not None diff --git a/fooof/tests/utils/test_io.py b/fooof/tests/utils/test_io.py index 83c5a76c3..41eca6bb0 100644 --- a/fooof/tests/utils/test_io.py +++ b/fooof/tests/utils/test_io.py @@ -1,5 +1,6 @@ """Test functions for fooof.utils.io.""" +import os import numpy as np from fooof.core.items import OBJ_DESC @@ -14,9 +15,9 @@ def test_load_fooof(): - file_name = 'test_fooof_all' + file_name = os.path.join(TEST_DATA_PATH, 'test_fooof_all') - tfm = load_fooof(file_name, TEST_DATA_PATH) + tfm = load_fooof(file_name) assert isinstance(tfm, FOOOF) @@ -32,8 +33,8 @@ def test_load_fooof(): def test_load_fooofgroup(): - file_name = 'test_fooofgroup_all' - tfg = load_fooofgroup(file_name, TEST_DATA_PATH) + file_name = os.path.join(TEST_DATA_PATH, 'test_fooofgroup_all') + tfg = load_fooofgroup(file_name) assert isinstance(tfg, FOOOFGroup)