def run(self):
tex_template = 'ps3_aggregator.tex.tpl'
report_tex_file_name = 'ps3_aggregator.tex'
self.pass_object('report_tex_file_name',report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
region_total = self.get_passed_object('region_session_total')
area_total = self.get_passed_object('area_session_total')
region_total = sorted(zip(region_total.keys(), region_total.values()))
region_total.append(('Total',sum([v[1] for v in region_total])))
area_total = sorted(zip(area_total.keys(), area_total.values()))
replace_dict = {
'<DATE>': datetime.date.today(),
'<FREQUENCY_PLOT_FILE>': 'ps3_frequency_aggregate_plots.pdf',
'<FREQUENCY_PROJECTION_PLOT_FILE>': 'ps3_frequency_projection_plots.pdf',
'<REGION_FREQUENCY_EXPERIMENT_COUNT_TABLE>': latex_table(self.get_passed_object('n_region_frequency_experiment')),
'<REGION_SESSION_TOTAL_DATA>': latex_table(region_total, hlines=False)
}
TextTemplateUtils.replace_template(template_file_name=tex_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
def run(self):
import TextTemplateUtils
import datetime
tex_template = 'ps_report.tex.tpl'
tex_session_template = 'ps_session.tex.tpl'
report_tex_file_name = self.pipeline.experiment + '-' + self.pipeline.subject + '-' + 'report.tex'
self.pass_object('report_tex_file_name',report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
tex_session_pages_str = ''
session_summary_array = self.get_passed_object('session_summary_array')
for session_summary in session_summary_array:
replace_dict = {'<SESS_NUM>': session_summary.sess_num,
'<PLOT_FILE>': self.pipeline.experiment + '-' + self.pipeline.subject + '-report_plot_' + session_summary.name + '.pdf',
'<STIMTAG>': session_summary.stimtag,
'<CONSTANT_NAME>': session_summary.constant_name,
'<CONSTANT_VALUE>': session_summary.constant_value,
'<CONSTANT_UNIT>': session_summary.constant_unit,
'<ISI_MID>': session_summary.isi_mid,
'<ISI_HALF_RANGE>': session_summary.isi_half_range,
'<PARAMETER1>': session_summary.parameter1,
'<PARAMETER2>': session_summary.parameter2,
'<FVALUE1>': '%.4f' % session_summary.anova_fvalues[0],
'<FVALUE2>': '%.4f' % session_summary.anova_fvalues[1],
'<FVALUE12>': '%.4f' % session_summary.anova_fvalues[2],
'<PVALUE1>': '%.4f' % session_summary.anova_pvalues[0],
'<PVALUE2>': '%.4f' % session_summary.anova_pvalues[1],
'<PVALUE12>': '%.4f' % session_summary.anova_pvalues[2]
}
tex_session_pages_str += TextTemplateUtils.replace_template_to_string(tex_session_template, replace_dict)
tex_session_pages_str += '\n'
session_data_tex_table = latex_table(self.get_passed_object('SESSION_DATA'))
replace_dict = {
'<SUBJECT>': self.pipeline.subject.replace('_', '\\textunderscore'),
'<EXPERIMENT>': self.pipeline.experiment,
'<DATE>': datetime.date.today(),
'<SESSION_DATA>': session_data_tex_table,
'<NUMBER_OF_SESSIONS>': self.get_passed_object('NUMBER_OF_SESSIONS'),
'<NUMBER_OF_ELECTRODES>': self.get_passed_object('NUMBER_OF_ELECTRODES'),
'<REPORT_PAGES>': tex_session_pages_str,
'<CUMULATIVE_ISI_MID>': self.get_passed_object('CUMULATIVE_ISI_MID'),
'<CUMULATIVE_ISI_HALF_RANGE>': self.get_passed_object('CUMULATIVE_ISI_HALF_RANGE'),
'<CUMULATIVE_PLOT_FILE>': self.pipeline.experiment + '-' + self.pipeline.subject + '-report_plot_Cumulative.pdf',
'<CUMULATIVE_PARAMETER1>': self.get_passed_object('CUMULATIVE_PARAMETER1'),
'<CUMULATIVE_PARAMETER2>': self.get_passed_object('CUMULATIVE_PARAMETER2')
}
TextTemplateUtils.replace_template(template_file_name=tex_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
tex_session_template = task + '_session.tex.tpl'
n_sess = self.get_passed_object('NUMBER_OF_SESSIONS')
n_bps = self.get_passed_object('NUMBER_OF_ELECTRODES')
session_summary_array = self.get_passed_object('session_summary_array')
report_tex_file_names = []
for i_sess in xrange(n_sess):
session_summary = session_summary_array[i_sess]
sess = session_summary.number
report_tex_file_name = '%s-%s-s%02d-report.tex' % (task,subject,sess)
report_tex_file_names.append(report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
replace_dict = {'<PROB_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-prob_recall_plot_' + session_summary.name + '.pdf',
'<STIM_AND_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-stim_and_recall_plot_' + session_summary.name + '.pdf',
'<IRT_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-irt_plot_' + session_summary.name + '.pdf',
'<DATE>': datetime.date.today(),
'<SUBJECT>': subject.replace('_','\\textunderscore'),
'<NUMBER_OF_ELECTRODES>': n_bps,
'<SESSION_NUMBER>': sess,
'<SESSION_DATE>': session_summary.date,
'<SESSION_LENGTH>': session_summary.length,
'<N_WORDS>': session_summary.n_words,
'<N_CORRECT_WORDS>': session_summary.n_correct_words,
'<PC_CORRECT_WORDS>': '%.2f' % session_summary.pc_correct_words,
'<N_PLI>': session_summary.n_pli,
'<PC_PLI>': '%.2f' % session_summary.pc_pli,
'<N_ELI>': session_summary.n_eli,
'<PC_ELI>': '%.2f' % session_summary.pc_eli,
'<N_MATH>': session_summary.n_math,
'<N_CORRECT_MATH>': session_summary.n_correct_math,
'<PC_CORRECT_MATH>': '%.2f' % session_summary.pc_correct_math,
'<MATH_PER_LIST>': '%.2f' % session_summary.math_per_list,
'<N_CORRECT_STIM>': session_summary.n_correct_stim,
'<N_TOTAL_STIM>': session_summary.n_total_stim,
'<PC_FROM_STIM>': '%.2f' % session_summary.pc_from_stim,
'<N_CORRECT_NONSTIM>': session_summary.n_correct_nonstim,
'<N_TOTAL_NONSTIM>': session_summary.n_total_nonstim,
'<PC_FROM_NONSTIM>': '%.2f' % session_summary.pc_from_nonstim,
'<CHISQR>': '%.2f' % session_summary.chisqr,
'<PVALUE>': '%.2f' % session_summary.pvalue,
'<N_STIM_INTR>': session_summary.n_stim_intr,
'<PC_FROM_STIM_INTR>': '%.2f' % session_summary.pc_from_stim_intr,
'<N_NONSTIM_INTR>': session_summary.n_nonstim_intr,
'<PC_FROM_NONSTIM_INTR>': '%.2f' % session_summary.pc_from_nonstim_intr,
'<CHISQR_INTR>': '%.2f' % session_summary.chisqr_intr,
'<PVALUE_INTR>': '%.2f' % session_summary.pvalue_intr
}
TextTemplateUtils.replace_template(template_file_name=tex_session_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
self.pass_object('report_tex_file_names', report_tex_file_names)
tex_combined_template = task + '_combined.tex.tpl'
combined_report_tex_file_name = '%s-%s-combined-report.tex' % (task,subject)
self.set_file_resources_to_move(combined_report_tex_file_name, dst='reports')
cumulative_summary = self.get_passed_object('cumulative_summary')
cumulative_data_tex_table = latex_table(self.get_passed_object('SESSION_DATA'))
replace_dict = {'<PROB_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-prob_recall_plot_combined.pdf',
'<IRT_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-irt_plot_combined.pdf',
'<DATE>': datetime.date.today(),
'<SESSION_DATA>': cumulative_data_tex_table,
'<SUBJECT>': subject.replace('_','\\textunderscore'),
'<NUMBER_OF_SESSIONS>': n_sess,
'<NUMBER_OF_ELECTRODES>': n_bps,
'<N_WORDS>': cumulative_summary.n_words,
'<N_CORRECT_WORDS>': cumulative_summary.n_correct_words,
'<PC_CORRECT_WORDS>': '%.2f' % cumulative_summary.pc_correct_words,
'<N_PLI>': cumulative_summary.n_pli,
'<PC_PLI>': '%.2f' % cumulative_summary.pc_pli,
'<N_ELI>': cumulative_summary.n_eli,
'<PC_ELI>': '%.2f' % cumulative_summary.pc_eli,
'<N_MATH>': cumulative_summary.n_math,
'<N_CORRECT_MATH>': cumulative_summary.n_correct_math,
'<PC_CORRECT_MATH>': '%.2f' % cumulative_summary.pc_correct_math,
'<MATH_PER_LIST>': '%.2f' % cumulative_summary.math_per_list,
'<N_CORRECT_STIM>': cumulative_summary.n_correct_stim,
'<N_TOTAL_STIM>': cumulative_summary.n_total_stim,
'<PC_FROM_STIM>': '%.2f' % cumulative_summary.pc_from_stim,
'<N_CORRECT_NONSTIM>': cumulative_summary.n_correct_nonstim,
'<N_TOTAL_NONSTIM>': cumulative_summary.n_total_nonstim,
'<PC_FROM_NONSTIM>': '%.2f' % cumulative_summary.pc_from_nonstim,
'<CHISQR>': '%.2f' % cumulative_summary.chisqr,
'<PVALUE>': '%.2f' % cumulative_summary.pvalue,
'<N_STIM_INTR>': cumulative_summary.n_stim_intr,
'<PC_FROM_STIM_INTR>': '%.2f' % cumulative_summary.pc_from_stim_intr,
'<N_NONSTIM_INTR>': cumulative_summary.n_nonstim_intr,
'<PC_FROM_NONSTIM_INTR>': '%.2f' % cumulative_summary.pc_from_nonstim_intr,
'<CHISQR_INTR>': '%.2f' % cumulative_summary.chisqr_intr,
'<PVALUE_INTR>': '%.2f' % cumulative_summary.pvalue_intr
}
TextTemplateUtils.replace_template(template_file_name=tex_combined_template, out_file_name=combined_report_tex_file_name, replace_dict=replace_dict)
self.pass_object('combined_report_tex_file_name', combined_report_tex_file_name)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
tex_session_template = task + "_session.tex.tpl"
n_sess = self.get_passed_object("NUMBER_OF_SESSIONS")
n_bps = self.get_passed_object("NUMBER_OF_ELECTRODES")
session_summary_array = self.get_passed_object("session_summary_array")
session_ttest_data = self.get_passed_object("session_ttest_data")
ttable_format = self.get_passed_object("ttable_format")
ttable_header = self.get_passed_object("ttable_header")
report_tex_file_names = []
for i_sess in xrange(n_sess):
session_summary = session_summary_array[i_sess]
sess = session_summary.number
report_tex_file_name = "%s-%s-s%02d-report.tex" % (task, subject, sess)
report_tex_file_names.append(report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst="reports")
session_ttest_tex_table = latex_table(session_ttest_data[i_sess])
replace_dict = {
"<PROB_RECALL_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-prob_recall_plot_"
+ session_summary.name
+ ".pdf",
"<IRT_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-irt_plot_"
+ session_summary.name
+ ".pdf",
"<DATE>": datetime.date.today(),
"<SUBJECT>": subject.replace("_", "\\textunderscore"),
"<NUMBER_OF_ELECTRODES>": n_bps,
"<SESSION_NUMBER>": sess,
"<SESSION_DATE>": session_summary.date,
"<SESSION_LENGTH>": session_summary.length,
"<N_WORDS>": session_summary.n_words,
"<N_CORRECT_WORDS>": session_summary.n_correct_words,
"<PC_CORRECT_WORDS>": "%.2f" % session_summary.pc_correct_words,
"<N_PLI>": session_summary.n_pli,
"<PC_PLI>": "%.2f" % session_summary.pc_pli,
"<N_ELI>": session_summary.n_eli,
"<PC_ELI>": "%.2f" % session_summary.pc_eli,
"<N_MATH>": session_summary.n_math,
"<N_CORRECT_MATH>": session_summary.n_correct_math,
"<PC_CORRECT_MATH>": "%.2f" % session_summary.pc_correct_math,
"<MATH_PER_LIST>": "%.2f" % session_summary.math_per_list,
"<TABLE_FORMAT>": ttable_format,
"<TABLE_HEADER>": ttable_header,
"<SIGNIFICANT_ELECTRODES>": session_ttest_tex_table,
"<AUC>": session_summary.auc,
"<ROC_AND_TERC_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-roc_and_terc_plot_"
+ session_summary.name
+ ".pdf",
}
TextTemplateUtils.replace_template(
template_file_name=tex_session_template, out_file_name=report_tex_file_name, replace_dict=replace_dict
)
self.pass_object("report_tex_file_names", report_tex_file_names)
tex_combined_template = task + "_combined.tex.tpl"
combined_report_tex_file_name = "%s-%s-combined-report.tex" % (task, subject)
self.set_file_resources_to_move(combined_report_tex_file_name, dst="reports")
cumulative_summary = self.get_passed_object("cumulative_summary")
cumulative_data_tex_table = latex_table(self.get_passed_object("SESSION_DATA"))
cumulative_ttest_tex_table = latex_table(self.get_passed_object("cumulative_ttest_data"))
replace_dict = {
"<PROB_RECALL_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-prob_recall_plot_combined.pdf",
"<IRT_PLOT_FILE>": self.pipeline.task + "-" + self.pipeline.subject + "-irt_plot_combined.pdf",
"<DATE>": datetime.date.today(),
"<SESSION_DATA>": cumulative_data_tex_table,
"<SUBJECT>": subject.replace("_", "\\textunderscore"),
"<NUMBER_OF_SESSIONS>": n_sess,
"<NUMBER_OF_ELECTRODES>": n_bps,
"<N_WORDS>": cumulative_summary.n_words,
"<N_CORRECT_WORDS>": cumulative_summary.n_correct_words,
"<PC_CORRECT_WORDS>": "%.2f" % cumulative_summary.pc_correct_words,
"<N_PLI>": cumulative_summary.n_pli,
"<PC_PLI>": "%.2f" % cumulative_summary.pc_pli,
"<N_ELI>": cumulative_summary.n_eli,
"<PC_ELI>": "%.2f" % cumulative_summary.pc_eli,
"<N_MATH>": cumulative_summary.n_math,
"<N_CORRECT_MATH>": cumulative_summary.n_correct_math,
"<PC_CORRECT_MATH>": "%.2f" % cumulative_summary.pc_correct_math,
"<MATH_PER_LIST>": "%.2f" % cumulative_summary.math_per_list,
"<TABLE_FORMAT>": ttable_format,
"<TABLE_HEADER>": ttable_header,
"<SIGNIFICANT_ELECTRODES>": cumulative_ttest_tex_table,
"<AUC>": cumulative_summary.auc,
"<PERM-P-VALUE>": cumulative_summary.perm_test_pvalue,
"<J-THRESH>": cumulative_summary.jstat_thresh,
"<J-PERC>": cumulative_summary.jstat_percentile,
"<ROC_AND_TERC_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-roc_and_terc_plot_combined.pdf",
}
TextTemplateUtils.replace_template(
template_file_name=tex_combined_template,
out_file_name=combined_report_tex_file_name,
replace_dict=replace_dict,
)
self.pass_object("combined_report_tex_file_name", combined_report_tex_file_name)
def run(self):
tex_template = 'ps_report.tex.tpl'
tex_session_template = 'ps_session.tex.tpl'
tex_ttest_table1_template = 'ttest_table1.tex.tpl'
tex_ttest_table2_template = 'ttest_table2.tex.tpl'
report_tex_file_name = self.pipeline.experiment + '-' + self.pipeline.subject + '-' + 'report.tex'
self.pass_object('report_tex_file_name',report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
param1_name = self.get_passed_object('param1_name')
param1_unit = self.get_passed_object('param1_unit')
param2_name = self.get_passed_object('param2_name')
param2_unit = self.get_passed_object('param2_unit')
const_param_name = self.get_passed_object('const_param_name')
const_unit = self.get_passed_object('const_unit')
cumulative_anova_fvalues = self.get_passed_object('CUMULATIVE_ANOVA_FVALUES')
cumulative_anova_pvalues = self.get_passed_object('CUMULATIVE_ANOVA_PVALUES')
cumulative_param1_ttest_table = self.get_passed_object('CUMULATIVE_PARAM1_TTEST_TABLE')
cumulative_param2_ttest_table = self.get_passed_object('CUMULATIVE_PARAM2_TTEST_TABLE')
cumulative_param12_ttest_table = self.get_passed_object('CUMULATIVE_PARAM12_TTEST_TABLE')
session_summary_array = self.get_passed_object('session_summary_array')
tex_session_pages_str = ''
for session_summary in session_summary_array:
n_ttest_tables = 0
param1_ttest_table = ''
if session_summary.param1_ttest_table is not None:
ttest_replace_dict = {'<PARAMETER>': param1_name,
'<UNIT>': param1_unit,
'<TABLE>': latex_table(session_summary.param1_ttest_table, hlines=False)
}
param1_ttest_table = TextTemplateUtils.replace_template_to_string(tex_ttest_table1_template, ttest_replace_dict)
n_ttest_tables += 1
param2_ttest_table = ''
if session_summary.param2_ttest_table is not None:
ttest_replace_dict = {'<PARAMETER>': param2_name,
'<UNIT>': param2_unit,
'<TABLE>': latex_table(session_summary.param2_ttest_table, hlines=False)
}
param2_ttest_table = TextTemplateUtils.replace_template_to_string(tex_ttest_table1_template, ttest_replace_dict)
n_ttest_tables += 1
param12_ttest_table = ''
if session_summary.param12_ttest_table is not None:
ttest_replace_dict = {'<PARAMETER1>': param1_name,
'<UNIT1>': param1_unit,
'<PARAMETER2>': param2_name,
'<UNIT2>': param2_unit,
'<TABLE>': latex_table(session_summary.param12_ttest_table, hlines=False)
}
param12_ttest_table = TextTemplateUtils.replace_template_to_string(tex_ttest_table2_template, ttest_replace_dict)
n_ttest_tables += 1
conditional_clearpage = '\\clearpage\n' if n_ttest_tables>0 else ''
replace_dict = {'<SESS_NUM>': session_summary.sess_num,
'<PLOT_FILE>': self.pipeline.experiment + '-' + self.pipeline.subject + '-report_plot_' + session_summary.name + '.pdf',
'<STIMTAG>': session_summary.stimtag,
'<REGION>': session_summary.region_of_interest,
'<CONSTANT_NAME>': const_param_name,
'<CONSTANT_VALUE>': session_summary.const_param_value,
'<CONSTANT_UNIT>': const_unit,
'<ISI_MID>': session_summary.isi_mid,
'<ISI_HALF_RANGE>': session_summary.isi_half_range,
'<PARAMETER1>': param1_name,
'<PARAMETER2>': param2_name,
'<FVALUE1>': '%.2f' % session_summary.anova_fvalues[0],
'<FVALUE2>': '%.2f' % session_summary.anova_fvalues[1],
'<FVALUE12>': '%.2f' % session_summary.anova_fvalues[2],
'<PVALUE1>': pvalue_formatting(session_summary.anova_pvalues[0]),
'<PVALUE2>': pvalue_formatting(session_summary.anova_pvalues[1]),
'<PVALUE12>': pvalue_formatting(session_summary.anova_pvalues[2]),
'<PARAM1_TTEST_TABLE>': param1_ttest_table,
'<PARAM2_TTEST_TABLE>': param2_ttest_table,
'<PARAM12_TTEST_TABLE>': param12_ttest_table,
'CONDITIONAL_CLEARPAGE': conditional_clearpage
}
tex_session_pages_str += TextTemplateUtils.replace_template_to_string(tex_session_template, replace_dict)
tex_session_pages_str += '\n'
session_data_tex_table = latex_table(self.get_passed_object('SESSION_DATA'))
xval_output = self.get_passed_object('xval_output')
perm_test_pvalue = self.get_passed_object('pvalue')
param1_ttest_table = ''
if cumulative_param1_ttest_table is not None:
ttest_replace_dict = {'<PARAMETER>': param1_name,
'<UNIT>': param1_unit,
'<TABLE>': latex_table(cumulative_param1_ttest_table, hlines=False)
}
param1_ttest_table = TextTemplateUtils.replace_template_to_string(tex_ttest_table1_template, ttest_replace_dict)
param2_ttest_table = ''
if cumulative_param2_ttest_table is not None:
ttest_replace_dict = {'<PARAMETER>': param2_name,
'<UNIT>': param2_unit,
'<TABLE>': latex_table(cumulative_param2_ttest_table, hlines=False)
}
param2_ttest_table = TextTemplateUtils.replace_template_to_string(tex_ttest_table1_template, ttest_replace_dict)
param12_ttest_table = ''
if cumulative_param12_ttest_table is not None:
ttest_replace_dict = {'<PARAMETER1>': param1_name,
'<UNIT1>': param1_unit,
'<PARAMETER2>': param2_name,
'<UNIT2>': param2_unit,
'<TABLE>': latex_table(cumulative_param12_ttest_table, hlines=False)
}
param12_ttest_table = TextTemplateUtils.replace_template_to_string(tex_ttest_table2_template, ttest_replace_dict)
replace_dict = {
'<SUBJECT>': self.pipeline.subject.replace('_', '\\textunderscore'),
'<EXPERIMENT>': self.pipeline.experiment,
'<DATE>': datetime.date.today(),
'<SESSION_DATA>': session_data_tex_table,
'<NUMBER_OF_SESSIONS>': self.get_passed_object('NUMBER_OF_SESSIONS'),
'<NUMBER_OF_ELECTRODES>': self.get_passed_object('NUMBER_OF_ELECTRODES'),
'<REPORT_PAGES>': tex_session_pages_str,
'<CUMULATIVE_ISI_MID>': self.get_passed_object('CUMULATIVE_ISI_MID'),
'<CUMULATIVE_ISI_HALF_RANGE>': self.get_passed_object('CUMULATIVE_ISI_HALF_RANGE'),
'<CUMULATIVE_PLOT_FILE>': self.pipeline.experiment + '-' + self.pipeline.subject + '-report_plot_Cumulative.pdf',
'<CUMULATIVE_PARAMETER1>': param1_name,
'<CUMULATIVE_PARAMETER2>': param2_name,
'<CUMULATIVE_FVALUE1>': '%.2f' % cumulative_anova_fvalues[0],
'<CUMULATIVE_FVALUE2>': '%.2f' % cumulative_anova_fvalues[1],
'<CUMULATIVE_FVALUE12>': '%.2f' % cumulative_anova_fvalues[2],
'<CUMULATIVE_PVALUE1>': pvalue_formatting(cumulative_anova_pvalues[0]),
'<CUMULATIVE_PVALUE2>': pvalue_formatting(cumulative_anova_pvalues[1]),
'<CUMULATIVE_PVALUE12>': pvalue_formatting(cumulative_anova_pvalues[2]),
'<CUMULATIVE_PARAM1_TTEST_TABLE>': param1_ttest_table,
'<CUMULATIVE_PARAM2_TTEST_TABLE>': param2_ttest_table,
'<CUMULATIVE_PARAM12_TTEST_TABLE>': param12_ttest_table,
'<AUC>': '%.2f' % (100*xval_output[-1].auc),
'<PERM-P-VALUE>': pvalue_formatting(perm_test_pvalue),
'<J-THRESH>': '%.3f' % xval_output[-1].jstat_thresh,
'<ROC_AND_TERC_PLOT_FILE>': self.pipeline.subject + '-roc_and_terc_plot_combined.pdf'
}
TextTemplateUtils.replace_template(template_file_name=tex_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
tex_session_template = task + '_session.tex.tpl'
n_sess = self.get_passed_object('NUMBER_OF_SESSIONS')
n_bps = self.get_passed_object('NUMBER_OF_ELECTRODES')
session_summary_array = self.get_passed_object('session_summary_array')
session_ttest_data = self.get_passed_object('session_ttest_data')
ttable_format = self.get_passed_object('ttable_format')
ttable_header = self.get_passed_object('ttable_header')
report_tex_file_names = []
for i_sess in xrange(n_sess):
session_summary = session_summary_array[i_sess]
sess = session_summary.number
report_tex_file_name = '%s-%s-s%02d-report.tex' % (task, subject,
sess)
report_tex_file_names.append(report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name,
dst='reports')
session_ttest_tex_table = latex_table(session_ttest_data[i_sess])
replace_dict = {
'<PROB_RECALL_PLOT_FILE>':
self.pipeline.task + '-' + self.pipeline.subject +
'-prob_recall_plot_' + session_summary.name + '.pdf',
'<IRT_PLOT_FILE>':
self.pipeline.task + '-' + self.pipeline.subject +
'-irt_plot_' + session_summary.name + '.pdf',
'<DATE>':
datetime.date.today(),
'<SUBJECT>':
subject.replace('_', '\\textunderscore'),
'<NUMBER_OF_ELECTRODES>':
n_bps,
'<SESSION_NUMBER>':
sess,
'<SESSION_DATE>':
session_summary.date,
'<SESSION_LENGTH>':
session_summary.length,
'<N_WORDS>':
session_summary.n_words,
'<N_CORRECT_WORDS>':
session_summary.n_correct_words,
'<PC_CORRECT_WORDS>':
'%.2f' % session_summary.pc_correct_words,
'<N_PLI>':
session_summary.n_pli,
'<PC_PLI>':
'%.2f' % session_summary.pc_pli,
'<N_ELI>':
session_summary.n_eli,
'<PC_ELI>':
'%.2f' % session_summary.pc_eli,
'<N_MATH>':
session_summary.n_math,
'<N_CORRECT_MATH>':
session_summary.n_correct_math,
'<PC_CORRECT_MATH>':
'%.2f' % session_summary.pc_correct_math,
'<MATH_PER_LIST>':
'%.2f' % session_summary.math_per_list,
'<TABLE_FORMAT>':
ttable_format,
'<TABLE_HEADER>':
ttable_header,
'<SIGNIFICANT_ELECTRODES>':
session_ttest_tex_table,
'<AUC>':
session_summary.auc,
'<ROC_AND_TERC_PLOT_FILE>':
self.pipeline.task + '-' + self.pipeline.subject +
'-roc_and_terc_plot_' + session_summary.name + '.pdf'
}
TextTemplateUtils.replace_template(
template_file_name=tex_session_template,
out_file_name=report_tex_file_name,
replace_dict=replace_dict)
self.pass_object('report_tex_file_names', report_tex_file_names)
tex_combined_template = task + '_combined.tex.tpl'
combined_report_tex_file_name = '%s-%s-combined-report.tex' % (task,
subject)
self.set_file_resources_to_move(combined_report_tex_file_name,
dst='reports')
cumulative_summary = self.get_passed_object('cumulative_summary')
cumulative_data_tex_table = latex_table(
self.get_passed_object('SESSION_DATA'))
cumulative_ttest_tex_table = latex_table(
self.get_passed_object('cumulative_ttest_data'))
replace_dict = {
'<PROB_RECALL_PLOT_FILE>':
self.pipeline.task + '-' + self.pipeline.subject +
'-prob_recall_plot_combined.pdf',
'<IRT_PLOT_FILE>':
self.pipeline.task + '-' + self.pipeline.subject +
'-irt_plot_combined.pdf',
'<DATE>':
datetime.date.today(),
'<SESSION_DATA>':
cumulative_data_tex_table,
'<SUBJECT>':
subject.replace('_', '\\textunderscore'),
'<NUMBER_OF_SESSIONS>':
n_sess,
'<NUMBER_OF_ELECTRODES>':
n_bps,
'<N_WORDS>':
cumulative_summary.n_words,
'<N_CORRECT_WORDS>':
cumulative_summary.n_correct_words,
'<PC_CORRECT_WORDS>':
'%.2f' % cumulative_summary.pc_correct_words,
'<N_PLI>':
cumulative_summary.n_pli,
'<PC_PLI>':
'%.2f' % cumulative_summary.pc_pli,
'<N_ELI>':
cumulative_summary.n_eli,
'<PC_ELI>':
'%.2f' % cumulative_summary.pc_eli,
'<N_MATH>':
cumulative_summary.n_math,
'<N_CORRECT_MATH>':
cumulative_summary.n_correct_math,
'<PC_CORRECT_MATH>':
'%.2f' % cumulative_summary.pc_correct_math,
'<MATH_PER_LIST>':
'%.2f' % cumulative_summary.math_per_list,
'<TABLE_FORMAT>':
ttable_format,
'<TABLE_HEADER>':
ttable_header,
'<SIGNIFICANT_ELECTRODES>':
cumulative_ttest_tex_table,
'<AUC>':
cumulative_summary.auc,
'<PERM-P-VALUE>':
cumulative_summary.perm_test_pvalue,
'<J-THRESH>':
cumulative_summary.jstat_thresh,
'<J-PERC>':
cumulative_summary.jstat_percentile,
'<ROC_AND_TERC_PLOT_FILE>':
self.pipeline.task + '-' + self.pipeline.subject +
'-roc_and_terc_plot_combined.pdf'
}
TextTemplateUtils.replace_template(
template_file_name=tex_combined_template,
out_file_name=combined_report_tex_file_name,
replace_dict=replace_dict)
self.pass_object('combined_report_tex_file_name',
combined_report_tex_file_name)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
tex_session_template = task + "_session.tex.tpl"
n_sess = self.get_passed_object("NUMBER_OF_SESSIONS")
n_bps = self.get_passed_object("NUMBER_OF_ELECTRODES")
session_summary_array = self.get_passed_object("session_summary_array")
report_tex_file_names = []
for i_sess in xrange(n_sess):
session_summary = session_summary_array[i_sess]
sess = session_summary.number
report_tex_file_name = "%s-%s-s%02d-report.tex" % (task, subject, sess)
report_tex_file_names.append(report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst="reports")
replace_dict = {
"<PROB_RECALL_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-prob_recall_plot_"
+ session_summary.name
+ ".pdf",
"<STIM_AND_RECALL_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-stim_and_recall_plot_"
+ session_summary.name
+ ".pdf",
"<IRT_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-irt_plot_"
+ session_summary.name
+ ".pdf",
"<DATE>": datetime.date.today(),
"<SUBJECT>": subject.replace("_", "\\textunderscore"),
"<NUMBER_OF_ELECTRODES>": n_bps,
"<SESSION_NUMBER>": sess,
"<SESSION_DATE>": session_summary.date,
"<SESSION_LENGTH>": session_summary.length,
"<N_WORDS>": session_summary.n_words,
"<N_CORRECT_WORDS>": session_summary.n_correct_words,
"<PC_CORRECT_WORDS>": "%.2f" % session_summary.pc_correct_words,
"<N_PLI>": session_summary.n_pli,
"<PC_PLI>": "%.2f" % session_summary.pc_pli,
"<N_ELI>": session_summary.n_eli,
"<PC_ELI>": "%.2f" % session_summary.pc_eli,
"<N_MATH>": session_summary.n_math,
"<N_CORRECT_MATH>": session_summary.n_correct_math,
"<PC_CORRECT_MATH>": "%.2f" % session_summary.pc_correct_math,
"<MATH_PER_LIST>": "%.2f" % session_summary.math_per_list,
"<N_CORRECT_STIM>": session_summary.n_correct_stim,
"<N_TOTAL_STIM>": session_summary.n_total_stim,
"<PC_FROM_STIM>": "%.2f" % session_summary.pc_from_stim,
"<N_CORRECT_NONSTIM>": session_summary.n_correct_nonstim,
"<N_TOTAL_NONSTIM>": session_summary.n_total_nonstim,
"<PC_FROM_NONSTIM>": "%.2f" % session_summary.pc_from_nonstim,
"<CHISQR>": "%.2f" % session_summary.chisqr,
"<PVALUE>": "%.2f" % session_summary.pvalue,
"<N_STIM_INTR>": session_summary.n_stim_intr,
"<PC_FROM_STIM_INTR>": "%.2f" % session_summary.pc_from_stim_intr,
"<N_NONSTIM_INTR>": session_summary.n_nonstim_intr,
"<PC_FROM_NONSTIM_INTR>": "%.2f" % session_summary.pc_from_nonstim_intr,
"<CHISQR_INTR>": "%.2f" % session_summary.chisqr_intr,
"<PVALUE_INTR>": "%.2f" % session_summary.pvalue_intr,
}
TextTemplateUtils.replace_template(
template_file_name=tex_session_template, out_file_name=report_tex_file_name, replace_dict=replace_dict
)
self.pass_object("report_tex_file_names", report_tex_file_names)
tex_combined_template = task + "_combined.tex.tpl"
combined_report_tex_file_name = "%s-%s-combined-report.tex" % (task, subject)
self.set_file_resources_to_move(combined_report_tex_file_name, dst="reports")
cumulative_summary = self.get_passed_object("cumulative_summary")
cumulative_data_tex_table = latex_table(self.get_passed_object("SESSION_DATA"))
replace_dict = {
"<PROB_RECALL_PLOT_FILE>": self.pipeline.task
+ "-"
+ self.pipeline.subject
+ "-prob_recall_plot_combined.pdf",
"<IRT_PLOT_FILE>": self.pipeline.task + "-" + self.pipeline.subject + "-irt_plot_combined.pdf",
"<DATE>": datetime.date.today(),
"<SESSION_DATA>": cumulative_data_tex_table,
"<SUBJECT>": subject.replace("_", "\\textunderscore"),
"<NUMBER_OF_SESSIONS>": n_sess,
"<NUMBER_OF_ELECTRODES>": n_bps,
"<N_WORDS>": cumulative_summary.n_words,
"<N_CORRECT_WORDS>": cumulative_summary.n_correct_words,
"<PC_CORRECT_WORDS>": "%.2f" % cumulative_summary.pc_correct_words,
"<N_PLI>": cumulative_summary.n_pli,
"<PC_PLI>": "%.2f" % cumulative_summary.pc_pli,
"<N_ELI>": cumulative_summary.n_eli,
"<PC_ELI>": "%.2f" % cumulative_summary.pc_eli,
"<N_MATH>": cumulative_summary.n_math,
"<N_CORRECT_MATH>": cumulative_summary.n_correct_math,
"<PC_CORRECT_MATH>": "%.2f" % cumulative_summary.pc_correct_math,
"<MATH_PER_LIST>": "%.2f" % cumulative_summary.math_per_list,
"<N_CORRECT_STIM>": cumulative_summary.n_correct_stim,
"<N_TOTAL_STIM>": cumulative_summary.n_total_stim,
"<PC_FROM_STIM>": "%.2f" % cumulative_summary.pc_from_stim,
"<N_CORRECT_NONSTIM>": cumulative_summary.n_correct_nonstim,
"<N_TOTAL_NONSTIM>": cumulative_summary.n_total_nonstim,
"<PC_FROM_NONSTIM>": "%.2f" % cumulative_summary.pc_from_nonstim,
"<CHISQR>": "%.2f" % cumulative_summary.chisqr,
"<PVALUE>": "%.2f" % cumulative_summary.pvalue,
"<N_STIM_INTR>": cumulative_summary.n_stim_intr,
"<PC_FROM_STIM_INTR>": "%.2f" % cumulative_summary.pc_from_stim_intr,
"<N_NONSTIM_INTR>": cumulative_summary.n_nonstim_intr,
"<PC_FROM_NONSTIM_INTR>": "%.2f" % cumulative_summary.pc_from_nonstim_intr,
"<CHISQR_INTR>": "%.2f" % cumulative_summary.chisqr_intr,
"<PVALUE_INTR>": "%.2f" % cumulative_summary.pvalue_intr,
}
TextTemplateUtils.replace_template(
template_file_name=tex_combined_template,
out_file_name=combined_report_tex_file_name,
replace_dict=replace_dict,
)
self.pass_object("combined_report_tex_file_name", combined_report_tex_file_name)
def run(self):
tex_template = 'ps_report.tex.tpl'
tex_session_template = 'ps_session.tex.tpl'
tex_ttest_table1_template = 'ttest_table1.tex.tpl'
tex_ttest_table2_template = 'ttest_table2.tex.tpl'
report_tex_file_name = self.pipeline.experiment + '-' + self.pipeline.subject + '-' + 'report.tex'
self.pass_object('report_tex_file_name', report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
param1_name = self.get_passed_object('param1_name')
param1_unit = self.get_passed_object('param1_unit')
param2_name = self.get_passed_object('param2_name')
param2_unit = self.get_passed_object('param2_unit')
const_param_name = self.get_passed_object('const_param_name')
const_unit = self.get_passed_object('const_unit')
cumulative_anova_fvalues = self.get_passed_object(
'CUMULATIVE_ANOVA_FVALUES')
cumulative_anova_pvalues = self.get_passed_object(
'CUMULATIVE_ANOVA_PVALUES')
cumulative_param1_ttest_table = self.get_passed_object(
'CUMULATIVE_PARAM1_TTEST_TABLE')
cumulative_param2_ttest_table = self.get_passed_object(
'CUMULATIVE_PARAM2_TTEST_TABLE')
cumulative_param12_ttest_table = self.get_passed_object(
'CUMULATIVE_PARAM12_TTEST_TABLE')
session_summary_array = self.get_passed_object('session_summary_array')
tex_session_pages_str = ''
for session_summary in session_summary_array:
n_ttest_tables = 0
param1_ttest_table = ''
if session_summary.param1_ttest_table is not None:
ttest_replace_dict = {
'<PARAMETER>':
param1_name,
'<UNIT>':
param1_unit,
'<TABLE>':
latex_table(session_summary.param1_ttest_table,
hlines=False)
}
param1_ttest_table = TextTemplateUtils.replace_template_to_string(
tex_ttest_table1_template, ttest_replace_dict)
n_ttest_tables += 1
param2_ttest_table = ''
if session_summary.param2_ttest_table is not None:
ttest_replace_dict = {
'<PARAMETER>':
param2_name,
'<UNIT>':
param2_unit,
'<TABLE>':
latex_table(session_summary.param2_ttest_table,
hlines=False)
}
param2_ttest_table = TextTemplateUtils.replace_template_to_string(
tex_ttest_table1_template, ttest_replace_dict)
n_ttest_tables += 1
param12_ttest_table = ''
if session_summary.param12_ttest_table is not None:
ttest_replace_dict = {
'<PARAMETER1>':
param1_name,
'<UNIT1>':
param1_unit,
'<PARAMETER2>':
param2_name,
'<UNIT2>':
param2_unit,
'<TABLE>':
latex_table(session_summary.param12_ttest_table,
hlines=False)
}
param12_ttest_table = TextTemplateUtils.replace_template_to_string(
tex_ttest_table2_template, ttest_replace_dict)
n_ttest_tables += 1
conditional_clearpage = '\\clearpage\n' if n_ttest_tables > 0 else ''
replace_dict = {
'<SESS_NUM>':
session_summary.sess_num,
'<PLOT_FILE>':
self.pipeline.experiment + '-' + self.pipeline.subject +
'-report_plot_' + session_summary.name + '.pdf',
'<STIMTAG>':
session_summary.stimtag,
'<REGION>':
session_summary.region_of_interest,
'<CONSTANT_NAME>':
const_param_name,
'<CONSTANT_VALUE>':
session_summary.const_param_value,
'<CONSTANT_UNIT>':
const_unit,
'<ISI_MID>':
session_summary.isi_mid,
'<ISI_HALF_RANGE>':
session_summary.isi_half_range,
'<PARAMETER1>':
param1_name,
'<PARAMETER2>':
param2_name,
'<FVALUE1>':
'%.2f' % session_summary.anova_fvalues[0],
'<FVALUE2>':
'%.2f' % session_summary.anova_fvalues[1],
'<FVALUE12>':
'%.2f' % session_summary.anova_fvalues[2],
'<PVALUE1>':
pvalue_formatting(session_summary.anova_pvalues[0]),
'<PVALUE2>':
pvalue_formatting(session_summary.anova_pvalues[1]),
'<PVALUE12>':
pvalue_formatting(session_summary.anova_pvalues[2]),
'<PARAM1_TTEST_TABLE>':
param1_ttest_table,
'<PARAM2_TTEST_TABLE>':
param2_ttest_table,
'<PARAM12_TTEST_TABLE>':
param12_ttest_table,
'CONDITIONAL_CLEARPAGE':
conditional_clearpage
}
tex_session_pages_str += TextTemplateUtils.replace_template_to_string(
tex_session_template, replace_dict)
tex_session_pages_str += '\n'
session_data_tex_table = latex_table(
self.get_passed_object('SESSION_DATA'))
xval_output = self.get_passed_object('xval_output')
perm_test_pvalue = self.get_passed_object('pvalue')
param1_ttest_table = ''
if cumulative_param1_ttest_table is not None:
ttest_replace_dict = {
'<PARAMETER>': param1_name,
'<UNIT>': param1_unit,
'<TABLE>': latex_table(cumulative_param1_ttest_table,
hlines=False)
}
param1_ttest_table = TextTemplateUtils.replace_template_to_string(
tex_ttest_table1_template, ttest_replace_dict)
param2_ttest_table = ''
if cumulative_param2_ttest_table is not None:
ttest_replace_dict = {
'<PARAMETER>': param2_name,
'<UNIT>': param2_unit,
'<TABLE>': latex_table(cumulative_param2_ttest_table,
hlines=False)
}
param2_ttest_table = TextTemplateUtils.replace_template_to_string(
tex_ttest_table1_template, ttest_replace_dict)
param12_ttest_table = ''
if cumulative_param12_ttest_table is not None:
ttest_replace_dict = {
'<PARAMETER1>':
param1_name,
'<UNIT1>':
param1_unit,
'<PARAMETER2>':
param2_name,
'<UNIT2>':
param2_unit,
'<TABLE>':
latex_table(cumulative_param12_ttest_table, hlines=False)
}
param12_ttest_table = TextTemplateUtils.replace_template_to_string(
tex_ttest_table2_template, ttest_replace_dict)
replace_dict = {
'<SUBJECT>':
self.pipeline.subject.replace('_', '\\textunderscore'),
'<EXPERIMENT>':
self.pipeline.experiment,
'<DATE>':
datetime.date.today(),
'<SESSION_DATA>':
session_data_tex_table,
'<NUMBER_OF_SESSIONS>':
self.get_passed_object('NUMBER_OF_SESSIONS'),
'<NUMBER_OF_ELECTRODES>':
self.get_passed_object('NUMBER_OF_ELECTRODES'),
'<REPORT_PAGES>':
tex_session_pages_str,
'<CUMULATIVE_ISI_MID>':
self.get_passed_object('CUMULATIVE_ISI_MID'),
'<CUMULATIVE_ISI_HALF_RANGE>':
self.get_passed_object('CUMULATIVE_ISI_HALF_RANGE'),
'<CUMULATIVE_PLOT_FILE>':
self.pipeline.experiment + '-' + self.pipeline.subject +
'-report_plot_Cumulative.pdf',
'<CUMULATIVE_PARAMETER1>':
param1_name,
'<CUMULATIVE_PARAMETER2>':
param2_name,
'<CUMULATIVE_FVALUE1>':
'%.2f' % cumulative_anova_fvalues[0],
'<CUMULATIVE_FVALUE2>':
'%.2f' % cumulative_anova_fvalues[1],
'<CUMULATIVE_FVALUE12>':
'%.2f' % cumulative_anova_fvalues[2],
'<CUMULATIVE_PVALUE1>':
pvalue_formatting(cumulative_anova_pvalues[0]),
'<CUMULATIVE_PVALUE2>':
pvalue_formatting(cumulative_anova_pvalues[1]),
'<CUMULATIVE_PVALUE12>':
pvalue_formatting(cumulative_anova_pvalues[2]),
'<CUMULATIVE_PARAM1_TTEST_TABLE>':
param1_ttest_table,
'<CUMULATIVE_PARAM2_TTEST_TABLE>':
param2_ttest_table,
'<CUMULATIVE_PARAM12_TTEST_TABLE>':
param12_ttest_table,
'<AUC>':
'%.2f' % (100 * xval_output[-1].auc),
'<PERM-P-VALUE>':
pvalue_formatting(perm_test_pvalue),
'<J-THRESH>':
'%.3f' % xval_output[-1].jstat_thresh,
'<ROC_AND_TERC_PLOT_FILE>':
self.pipeline.subject + '-roc_and_terc_plot_combined.pdf'
}
TextTemplateUtils.replace_template(template_file_name=tex_template,
out_file_name=report_tex_file_name,
replace_dict=replace_dict)
def run(self):
tex_template = 'ps_aggregator.tex.tpl'
report_tex_file_name = 'ps_aggregator.tex'
self.pass_object('report_tex_file_name',report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
region_total = self.get_passed_object('region_session_total')
area_total = self.get_passed_object('area_session_total')
region_total = sorted(zip(region_total.keys(), region_total.values()))
region_total.append(('Total',sum([v[1] for v in region_total])))
area_total = sorted(zip(area_total.keys(), area_total.values()))
# fvalue_rf = self.get_passed_object('fvalue_rf')
# pvalue_rf = self.get_passed_object('pvalue_rf')
#
# fvalue_ra_low = self.get_passed_object('fvalue_ra_low')
# pvalue_ra_low = self.get_passed_object('pvalue_ra_low')
#
# fvalue_ra_high = self.get_passed_object('fvalue_ra_high')
# pvalue_ra_high = self.get_passed_object('pvalue_ra_high')
#
# fvalue_rd_low = self.get_passed_object('fvalue_rd_low')
# pvalue_rd_low = self.get_passed_object('pvalue_rd_low')
#
# fvalue_rd_high = self.get_passed_object('fvalue_rd_high')
# pvalue_rd_high = self.get_passed_object('pvalue_rd_high')
# replace_dict = {
# '<DATE>': datetime.date.today(),
# '<FREQUENCY_PLOT_FILE>': 'ps_frequency_aggregate_plots.pdf',
# '<FVALUERF1>': '%.2f' % fvalue_rf[0],
# '<FVALUERF2>': '%.2f' % fvalue_rf[1],
# '<FVALUERF12>': '%.2f' % fvalue_rf[2],
# '<PVALUERF1>': pvalue_formatting(pvalue_rf[0]),
# '<PVALUERF2>': pvalue_formatting(pvalue_rf[1]),
# '<PVALUERF12>': pvalue_formatting(pvalue_rf[2]),
# '<AMPLITUDE_LOW_PLOT_FILE>': 'ps_amplitude_low_aggregate_plots.pdf',
# '<FVALUERALOW1>': '%.2f' % fvalue_ra_low[0],
# '<FVALUERALOW2>': '%.2f' % fvalue_ra_low[1],
# '<FVALUERALOW12>': '%.2f' % fvalue_ra_low[2],
# '<PVALUERALOW1>': pvalue_formatting(pvalue_ra_low[0]),
# '<PVALUERALOW2>': pvalue_formatting(pvalue_ra_low[1]),
# '<PVALUERALOW12>': pvalue_formatting(pvalue_ra_low[2]),
# '<AMPLITUDE_HIGH_PLOT_FILE>': 'ps_amplitude_high_aggregate_plots.pdf',
# '<FVALUERAHIGH1>': '%.2f' % fvalue_ra_high[0],
# '<FVALUERAHIGH2>': '%.2f' % fvalue_ra_high[1],
# '<FVALUERAHIGH12>': '%.2f' % fvalue_ra_high[2],
# '<PVALUERAHIGH1>': pvalue_formatting(pvalue_ra_high[0]),
# '<PVALUERAHIGH2>': pvalue_formatting(pvalue_ra_high[1]),
# '<PVALUERAHIGH12>': pvalue_formatting(pvalue_ra_high[2]),
# '<DURATION_LOW_PLOT_FILE>': 'ps_duration_low_aggregate_plots.pdf',
# '<FVALUERDLOW1>': '%.2f' % fvalue_rd_low[0],
# '<FVALUERDLOW2>': '%.2f' % fvalue_rd_low[1],
# '<FVALUERDLOW12>': '%.2f' % fvalue_rd_low[2],
# '<PVALUERDLOW1>': pvalue_formatting(pvalue_rd_low[0]),
# '<PVALUERDLOW2>': pvalue_formatting(pvalue_rd_low[1]),
# '<PVALUERDLOW12>': pvalue_formatting(pvalue_rd_low[2]),
# '<DURATION_HIGH_PLOT_FILE>': 'ps_duration_high_aggregate_plots.pdf',
# '<FVALUERDHIGH1>': '%.2f' % fvalue_rd_high[0],
# '<FVALUERDHIGH2>': '%.2f' % fvalue_rd_high[1],
# '<FVALUERDHIGH12>': '%.2f' % fvalue_rd_high[2],
# '<PVALUERDHIGH1>': pvalue_formatting(pvalue_rd_high[0]),
# '<PVALUERDHIGH2>': pvalue_formatting(pvalue_rd_high[1]),
# '<PVALUERDHIGH12>': pvalue_formatting(pvalue_rd_high[2]),
# '<REGION_SESSION_TOTAL_DATA>': latex_table(region_total, hlines=False)
# }
replace_dict = {
'<DATE>': datetime.date.today(),
# '<FREQUENCY_PLOT_FILE>': 'ps_frequency_aggregate_plots.pdf',
'<CENTRALIZED_FREQUENCY_PLOT_FILE>': 'ps_centralized_frequency_aggregate_plots.pdf',
'<FREQUENCY_PROJECTION_PLOT_FILE>': 'ps_frequency_projection_plots.pdf',
'<REGION_FREQUENCY_EXPERIMENT_COUNT_TABLE>': latex_table(self.get_passed_object('n_region_frequency_experiment')),
'<FVALUERF1>': '%.2f' % np.nan,
'<FVALUERF2>': '%.2f' % np.nan,
'<FVALUERF12>': '%.2f' % np.nan,
'<PVALUERF1>': pvalue_formatting(np.nan),
'<PVALUERF2>': pvalue_formatting(np.nan),
'<PVALUERF12>': pvalue_formatting(np.nan),
'<AMPLITUDE_LOW_PLOT_FILE>': 'ps_amplitude_low_aggregate_plots.pdf',
'<FVALUERALOW1>': '%.2f' % np.nan,
'<FVALUERALOW2>': '%.2f' % np.nan,
'<FVALUERALOW12>': '%.2f' % np.nan,
'<PVALUERALOW1>': pvalue_formatting(np.nan),
'<PVALUERALOW2>': pvalue_formatting(np.nan),
'<PVALUERALOW12>': pvalue_formatting(np.nan),
'<AMPLITUDE_HIGH_PLOT_FILE>': 'ps_amplitude_high_aggregate_plots.pdf',
'<FVALUERAHIGH1>': '%.2f' % np.nan,
'<FVALUERAHIGH2>': '%.2f' % np.nan,
'<FVALUERAHIGH12>': '%.2f' % np.nan,
'<PVALUERAHIGH1>': pvalue_formatting(np.nan),
'<PVALUERAHIGH2>': pvalue_formatting(np.nan),
'<PVALUERAHIGH12>': pvalue_formatting(np.nan),
'<DURATION_LOW_PLOT_FILE>': 'ps_duration_low_aggregate_plots.pdf',
'<FVALUERDLOW1>': '%.2f' % np.nan,
'<FVALUERDLOW2>': '%.2f' % np.nan,
'<FVALUERDLOW12>': '%.2f' % np.nan,
'<PVALUERDLOW1>': pvalue_formatting(np.nan),
'<PVALUERDLOW2>': pvalue_formatting(np.nan),
'<PVALUERDLOW12>': pvalue_formatting(np.nan),
'<DURATION_HIGH_PLOT_FILE>': 'ps_duration_high_aggregate_plots.pdf',
'<FVALUERDHIGH1>': '%.2f' % np.nan,
'<FVALUERDHIGH2>': '%.2f' % np.nan,
'<FVALUERDHIGH12>': '%.2f' % np.nan,
'<PVALUERDHIGH1>': pvalue_formatting(np.nan),
'<PVALUERDHIGH2>': pvalue_formatting(np.nan),
'<PVALUERDHIGH12>': pvalue_formatting(np.nan),
'<REGION_SESSION_TOTAL_DATA>': latex_table(region_total, hlines=False)
}
TextTemplateUtils.replace_template(template_file_name=tex_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
events = self.get_passed_object(task + '_events')
tal_info = self.get_passed_object('tal_info')
#channels = self.get_passed_object('channels')
n_bps = len(tal_info)
n_chs = 128 #len(channels)
bpmat = np.zeros(shape=(n_chs, n_bps), dtype=np.float)
for i,bp in enumerate(tal_info):
e1, e2 = bp['channel_str']
bpmat[int(e1)-1, i] = 1
bpmat[int(e2)-1, i] = -1
lr_classifier = self.get_passed_object('lr_classifier')
xval_output = self.get_passed_object('xval_output')[-1]
probs = xval_output.probs
thresh = xval_output.jstat_thresh
mat_filename = '%s_%s_%s.biomarker.mat' % (subject, datetime.date.today(), task)
mdict = {'Bio': {'Subject': subject,
'Version': self.params.version,
'Sessions': np.unique(events.session),
'W': lr_classifier.coef_[0],
'W0': lr_classifier.intercept_[0],
'trainingProb': probs[:,None],
'thresh': thresh,
'bpmat': bpmat,
'freqs': self.params.freqs,
'fs': self.get_passed_object('samplerate'),
'StimParams': {'elec1': self.params.stim_params.elec1,
'elec2': self.params.stim_params.elec2,
'amplitude': self.params.stim_params.amplitude,
'duration': self.params.stim_params.duration,
'trainFrequency': self.params.stim_params.trainFrequency,
'trainCount' : self.params.stim_params.trainCount,
'pulseFrequency': self.params.stim_params.pulseFrequency,
'pulseCount': self.params.stim_params.pulseCount},
'filename': mat_filename}}
mat_filename_in_workspace = self.get_path_to_resource_in_workspace(mat_filename)
savemat(mat_filename_in_workspace, mdict)
replace_dict = {
'load FILL_IN': 'load ' + mat_filename
}
#stat_accum_in_workspace = self.get_path_to_resource_in_workspace('StatAccum.m')
#TextTemplateUtils.replace_template(template_file_name='StatAccum.m', out_file_name=stat_accum_in_workspace, replace_dict=replace_dict)
stim_control_in_workspace = self.get_path_to_resource_in_workspace('StimControl.m')
TextTemplateUtils.replace_template(template_file_name='StimControl.m', out_file_name=stim_control_in_workspace, replace_dict=replace_dict)
self.biomarker_components += [stim_control_in_workspace, mat_filename_in_workspace]
zip_list = ' '.join(self.biomarker_components)
biomarker_filename_in_workspace = mat_filename_in_workspace[:-4] # cutoff .mat
print 'Zipping biomarker file', biomarker_filename_in_workspace
zip_command_str = 'zip -9 -j %s %s' % (biomarker_filename_in_workspace, zip_list)
call([zip_command_str], shell=True)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
tex_session_template = task + '_session.tex.tpl'
n_sess = self.get_passed_object('NUMBER_OF_SESSIONS')
n_bps = self.get_passed_object('NUMBER_OF_ELECTRODES')
session_summary_array = self.get_passed_object('session_summary_array')
session_ttest_data = self.get_passed_object('session_ttest_data')
ttable_format = self.get_passed_object('ttable_format')
ttable_header = self.get_passed_object('ttable_header')
report_tex_file_names = []
for i_sess in xrange(n_sess):
session_summary = session_summary_array[i_sess]
sess = session_summary.number
report_tex_file_name = '%s-%s-s%02d-report.tex' % (task,subject,sess)
report_tex_file_names.append(report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
session_ttest_tex_table = latex_table(session_ttest_data[i_sess])
replace_dict = {'<PROB_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-prob_recall_plot_' + session_summary.name + '.pdf',
'<IRT_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-irt_plot_' + session_summary.name + '.pdf',
'<DATE>': datetime.date.today(),
'<SUBJECT>': subject.replace('_','\\textunderscore'),
'<NUMBER_OF_ELECTRODES>': n_bps,
'<SESSION_NUMBER>': sess,
'<SESSION_DATE>': session_summary.date,
'<SESSION_LENGTH>': session_summary.length,
'<N_WORDS>': session_summary.n_words,
'<N_CORRECT_WORDS>': session_summary.n_correct_words,
'<PC_CORRECT_WORDS>': '%.2f' % session_summary.pc_correct_words,
'<N_PLI>': session_summary.n_pli,
'<PC_PLI>': '%.2f' % session_summary.pc_pli,
'<N_ELI>': session_summary.n_eli,
'<PC_ELI>': '%.2f' % session_summary.pc_eli,
'<N_MATH>': session_summary.n_math,
'<N_CORRECT_MATH>': session_summary.n_correct_math,
'<PC_CORRECT_MATH>': '%.2f' % session_summary.pc_correct_math,
'<MATH_PER_LIST>': '%.2f' % session_summary.math_per_list,
'<TABLE_FORMAT>': ttable_format,
'<TABLE_HEADER>': ttable_header,
'<SIGNIFICANT_ELECTRODES>': session_ttest_tex_table,
'<AUC>': session_summary.auc,
'<ROC_AND_TERC_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-roc_and_terc_plot_' + session_summary.name + '.pdf'
}
TextTemplateUtils.replace_template(template_file_name=tex_session_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
self.pass_object('report_tex_file_names', report_tex_file_names)
tex_combined_template = task + '_combined.tex.tpl'
combined_report_tex_file_name = '%s-%s-combined-report.tex' % (task,subject)
self.set_file_resources_to_move(combined_report_tex_file_name, dst='reports')
cumulative_summary = self.get_passed_object('cumulative_summary')
cumulative_data_tex_table = latex_table(self.get_passed_object('SESSION_DATA'))
cumulative_ttest_tex_table = latex_table(self.get_passed_object('cumulative_ttest_data'))
replace_dict = {'<PROB_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-prob_recall_plot_combined.pdf',
'<IRT_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-irt_plot_combined.pdf',
'<DATE>': datetime.date.today(),
'<SESSION_DATA>': cumulative_data_tex_table,
'<SUBJECT>': subject.replace('_','\\textunderscore'),
'<NUMBER_OF_SESSIONS>': n_sess,
'<NUMBER_OF_ELECTRODES>': n_bps,
'<N_WORDS>': cumulative_summary.n_words,
'<N_CORRECT_WORDS>': cumulative_summary.n_correct_words,
'<PC_CORRECT_WORDS>': '%.2f' % cumulative_summary.pc_correct_words,
'<N_PLI>': cumulative_summary.n_pli,
'<PC_PLI>': '%.2f' % cumulative_summary.pc_pli,
'<N_ELI>': cumulative_summary.n_eli,
'<PC_ELI>': '%.2f' % cumulative_summary.pc_eli,
'<N_MATH>': cumulative_summary.n_math,
'<N_CORRECT_MATH>': cumulative_summary.n_correct_math,
'<PC_CORRECT_MATH>': '%.2f' % cumulative_summary.pc_correct_math,
'<MATH_PER_LIST>': '%.2f' % cumulative_summary.math_per_list,
'<TABLE_FORMAT>': ttable_format,
'<TABLE_HEADER>': ttable_header,
'<SIGNIFICANT_ELECTRODES>': cumulative_ttest_tex_table,
'<AUC>': cumulative_summary.auc,
'<PERM-P-VALUE>': cumulative_summary.perm_test_pvalue,
'<J-THRESH>': cumulative_summary.jstat_thresh,
'<J-PERC>': cumulative_summary.jstat_percentile,
'<ROC_AND_TERC_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-roc_and_terc_plot_combined.pdf'
}
TextTemplateUtils.replace_template(template_file_name=tex_combined_template, out_file_name=combined_report_tex_file_name, replace_dict=replace_dict)
self.pass_object('combined_report_tex_file_name', combined_report_tex_file_name)
def run(self):
subject = self.pipeline.subject
task = self.pipeline.task
tex_session_template = task + '_session.tex.tpl'
n_sess = self.get_passed_object('NUMBER_OF_SESSIONS')
n_bps = self.get_passed_object('NUMBER_OF_ELECTRODES')
session_summary_array = self.get_passed_object('session_summary_array')
report_tex_file_names = []
for i_sess in xrange(n_sess):
session_summary = session_summary_array[i_sess]
sess = session_summary.number
report_tex_file_name = '%s-%s-s%02d-report.tex' % (task,subject,sess)
report_tex_file_names.append(report_tex_file_name)
self.set_file_resources_to_move(report_tex_file_name, dst='reports')
replace_dict = {'<PROB_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-prob_recall_plot_' + session_summary.name + '.pdf',
'<STIM_AND_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-stim_and_recall_plot_' + session_summary.name + '.pdf',
'<IRT_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-irt_plot_' + session_summary.name + '.pdf',
'<DATE>': datetime.date.today(),
'<SUBJECT>': subject.replace('_','\\textunderscore'),
'<NUMBER_OF_ELECTRODES>': n_bps,
'<SESSION_NUMBER>': sess,
'<SESSION_DATE>': session_summary.date,
'<SESSION_LENGTH>': session_summary.length,
'<N_WORDS>': session_summary.n_words,
'<N_CORRECT_WORDS>': session_summary.n_correct_words,
'<PC_CORRECT_WORDS>': '%.2f' % session_summary.pc_correct_words,
'<N_PLI>': session_summary.n_pli,
'<PC_PLI>': '%.2f' % session_summary.pc_pli,
'<N_ELI>': session_summary.n_eli,
'<PC_ELI>': '%.2f' % session_summary.pc_eli,
'<N_MATH>': session_summary.n_math,
'<N_CORRECT_MATH>': session_summary.n_correct_math,
'<PC_CORRECT_MATH>': '%.2f' % session_summary.pc_correct_math,
'<MATH_PER_LIST>': '%.2f' % session_summary.math_per_list,
'<N_CORRECT_STIM>': session_summary.n_correct_stim,
'<N_TOTAL_STIM>': session_summary.n_total_stim,
'<PC_FROM_STIM>': '%.2f' % session_summary.pc_from_stim,
'<N_CORRECT_NONSTIM>': session_summary.n_correct_nonstim,
'<N_TOTAL_NONSTIM>': session_summary.n_total_nonstim,
'<PC_FROM_NONSTIM>': '%.2f' % session_summary.pc_from_nonstim,
'<CHISQR>': '%.2f' % session_summary.chisqr,
'<PVALUE>': '%.2f' % session_summary.pvalue,
'<N_STIM_INTR>': session_summary.n_stim_intr,
'<PC_FROM_STIM_INTR>': '%.2f' % session_summary.pc_from_stim_intr,
'<N_NONSTIM_INTR>': session_summary.n_nonstim_intr,
'<PC_FROM_NONSTIM_INTR>': '%.2f' % session_summary.pc_from_nonstim_intr,
'<CHISQR_INTR>': '%.2f' % session_summary.chisqr_intr,
'<PVALUE_INTR>': '%.2f' % session_summary.pvalue_intr
}
TextTemplateUtils.replace_template(template_file_name=tex_session_template, out_file_name=report_tex_file_name, replace_dict=replace_dict)
self.pass_object('report_tex_file_names', report_tex_file_names)
tex_combined_template = task + '_combined.tex.tpl'
combined_report_tex_file_name = '%s-%s-combined-report.tex' % (task,subject)
self.set_file_resources_to_move(combined_report_tex_file_name, dst='reports')
cumulative_summary = self.get_passed_object('cumulative_summary')
cumulative_data_tex_table = latex_table(self.get_passed_object('SESSION_DATA'))
replace_dict = {'<PROB_RECALL_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-prob_recall_plot_combined.pdf',
'<IRT_PLOT_FILE>': self.pipeline.task + '-' + self.pipeline.subject + '-irt_plot_combined.pdf',
'<DATE>': datetime.date.today(),
'<SESSION_DATA>': cumulative_data_tex_table,
'<SUBJECT>': subject.replace('_','\\textunderscore'),
'<NUMBER_OF_SESSIONS>': n_sess,
'<NUMBER_OF_ELECTRODES>': n_bps,
'<N_WORDS>': cumulative_summary.n_words,
'<N_CORRECT_WORDS>': cumulative_summary.n_correct_words,
'<PC_CORRECT_WORDS>': '%.2f' % cumulative_summary.pc_correct_words,
'<N_PLI>': cumulative_summary.n_pli,
'<PC_PLI>': '%.2f' % cumulative_summary.pc_pli,
'<N_ELI>': cumulative_summary.n_eli,
'<PC_ELI>': '%.2f' % cumulative_summary.pc_eli,
'<N_MATH>': cumulative_summary.n_math,
'<N_CORRECT_MATH>': cumulative_summary.n_correct_math,
'<PC_CORRECT_MATH>': '%.2f' % cumulative_summary.pc_correct_math,
'<MATH_PER_LIST>': '%.2f' % cumulative_summary.math_per_list,
'<N_CORRECT_STIM>': cumulative_summary.n_correct_stim,
'<N_TOTAL_STIM>': cumulative_summary.n_total_stim,
'<PC_FROM_STIM>': '%.2f' % cumulative_summary.pc_from_stim,
'<N_CORRECT_NONSTIM>': cumulative_summary.n_correct_nonstim,
'<N_TOTAL_NONSTIM>': cumulative_summary.n_total_nonstim,
'<PC_FROM_NONSTIM>': '%.2f' % cumulative_summary.pc_from_nonstim,
'<CHISQR>': '%.2f' % cumulative_summary.chisqr,
'<PVALUE>': '%.2f' % cumulative_summary.pvalue,
'<N_STIM_INTR>': cumulative_summary.n_stim_intr,
'<PC_FROM_STIM_INTR>': '%.2f' % cumulative_summary.pc_from_stim_intr,
'<N_NONSTIM_INTR>': cumulative_summary.n_nonstim_intr,
'<PC_FROM_NONSTIM_INTR>': '%.2f' % cumulative_summary.pc_from_nonstim_intr,
'<CHISQR_INTR>': '%.2f' % cumulative_summary.chisqr_intr,
'<PVALUE_INTR>': '%.2f' % cumulative_summary.pvalue_intr
}
TextTemplateUtils.replace_template(template_file_name=tex_combined_template, out_file_name=combined_report_tex_file_name, replace_dict=replace_dict)
self.pass_object('combined_report_tex_file_name', combined_report_tex_file_name)
