def plot_between_within_box_plot(metric, where, filename):
conn = sqlite3.connect(dbfile)
c = conn.cursor()
metric_vals = []
where_keys = " and ".join([t[0] + "=?" for t in where])
c.execute("SELECT %s FROM reliability2010_within_subjects where %s ORDER BY subject_id"%(metric,where_keys), tuple([t[1] for t in where]))
metric_vals.append(np.array(c.fetchall()))
where_keys = " and ".join([t[0] + "=?" for t in where])
exclude = []
exclude_str = ""
for key in [t[1] for t in where if t[0] == "contrast_name"]:
if key.lower().find('finger') != -1 or key.lower().find('foot') != -1:
exclude = lefties
break
if exclude:
#exclude_str = " and (subject_id1 not in (%s) and subject_id2 not in (%s))"%(",".join(["'%s'"%s for s in exclude]), )*2
exclude_str = " and ((subject_id1 not in (%s) and subject_id2 not in (%s)) or (subject_id1 in (%s) and subject_id2 in (%s)))"%((",".join(["'%s'"%s for s in exclude]), )*4)
c.execute("SELECT %s FROM reliability2010_between_subjects where %s"%(metric,where_keys) + exclude_str, tuple([t[1] for t in where]))
arr = np.array(c.fetchall())
metric_vals.append(arr)
conn.commit()
c.close()
fig = plt.figure()
figtitle = ", ".join([t[0] + "=" + str(t[1]) for t in where])
t = fig.text(0.5, 0.95, figtitle,
horizontalalignment='center',
fontproperties=mpl.font_manager.FontProperties(size=16))
ax1 = fig.add_subplot(111)
ax1.boxplot(metric_vals)
ax1.set_xticklabels(["within subjects", "between subjects"])
ax1.set_ylabel(metric + " overlap")
ax1.set_ylim(bottom=-0.1, top=1.1)
if not os.path.exists(os.path.dirname(filename)):
os.makedirs(os.path.dirname(filename))
ax1.text(0.5, 0.90, "onesided_p = %.2f, twosided_p = %.2f"%two_sample(metric_vals[1], metric_vals[0]),
horizontalalignment='center',
fontproperties=mpl.font_manager.FontProperties(size=16),
transform=ax1.transAxes)
plt.savefig(filename)
def plot_between_session_box_plot(metric, where, compare, exclude, filename, table='reliability2010_within_subjects', test = True):
conn = sqlite3.connect(dbfile)
c = conn.cursor()
metric_vals = []
where_keys = " and ".join([t[0] + "=?" for t in where])
c.execute("SELECT DISTINCT subject_id FROM %s where %s and %s in (%s) and dice = 0 and distance is NULL ORDER BY subject_id"%(table,where_keys, compare[0], ','.join(["'%s'"%s for s in compare[1]])), tuple([t[1] for t in where]))
exclude = ('subject_id', exclude[1] + [i[0] for i in c.fetchall()])
for compare_c in compare[1]:
where_keys = " and ".join([t[0] + "=?" for t in where+[compare]])
exclude_clause = "%s not in (%s)"%(exclude[0], ",".join(["'%s'"%s for s in exclude[1]]))
c.execute("SELECT %s FROM %s where %s ORDER BY subject_id"%(metric,table,where_keys+ " and " +exclude_clause), tuple([t[1] for t in where] + [compare_c]))
metric_vals.append(np.array(c.fetchall(), dtype=np.float))
c.execute("SELECT DISTINCT subject_id FROM reliability2010_within_subjects WHERE %s"%exclude_clause)
subject_ids = c.fetchall()
if len(subject_ids) < 2:
return
conn.commit()
c.close()
metric_vals = np.array(metric_vals, dtype=np.float)
metric_vals.shape = (metric_vals.shape[0], metric_vals.shape[1])
fig = plt.figure(figsize=(8.27,11.69))
figtitle = ", ".join([t[0] + "=" + str(t[1]) for t in where])
t = fig.text(0.5, 0.95, figtitle,
horizontalalignment='center',
fontproperties=mpl.font_manager.FontProperties(size=16))
ax1 = fig.add_subplot(212)
ax1.boxplot(metric_vals.T)
ax1.set_xticklabels(compare[1])
ax1.set_ylabel(metric + " overlap")
#ax1.set_ylim(bottom=-0.1, top=1.1)
subject_ids =[subject_id[0].split('-')[0] for subject_id in subject_ids]
ax2 = fig.add_subplot(211)
colormap = plt.cm.spectral
ax2.set_color_cycle([colormap(i) for i in np.linspace(0, 0.9, len(subject_ids))])
ax2.plot(range(1,len(compare[1])+1), metric_vals, marker = 'o')
ax2.set_ylabel(metric + " overlap")
ax2.set_xlim(ax1.get_xlim())
ax2.set_ylim(ax1.get_ylim())
ax2.get_xaxis().set_visible(False)
ax2.legend(subject_ids, title="Subjects",
#bbox_to_anchor=(0., 1.02, 1., .102), loc=9,
ncol=4,
mode="expand",
borderaxespad=0.)
if not os.path.exists(os.path.dirname(filename)):
os.makedirs(os.path.dirname(filename))
if test:
ax1.text(0.5, 0.90, "onesided_p = %.2f, twosided_p = %.2f"%paired_one_sample(metric_vals[1,:],
metric_vals[0,:],
func=hdmedian),
horizontalalignment='center',
fontproperties=mpl.font_manager.FontProperties(size=16),
transform=ax1.transAxes)
print figtitle
conn = sqlite3.connect(dbfile)
c = conn.cursor()
insert_vals = dict(where)
insert_vals['metric'] = metric
parameters = {'hdmedian': hdmedian,
#'IQR': hdIQR,
'tmean': lambda v:trimr(v, (0.2,0.2)).mean(),
#'winsorized_variance': lambda v:winsorize(v, (0.2,0.2)).var()
}
for parameter,func in parameters.iteritems():
if parameter in ['IQR', 'winsorized_variance']:
_, insert_vals['twosided_p'], insert_vals['ci_l'], insert_vals['ci_h'] = two_sample(metric_vals[1,:], metric_vals[0,:], func = func, ci = True)
else:
_, insert_vals['twosided_p'], insert_vals['ci_l'], insert_vals['ci_h'] = paired_one_sample(metric_vals[1,:], metric_vals[0,:], func = func, ci = True)
insert_vals['parameter'] = parameter
insert_vals['value_1'] = float(func(metric_vals[0,:]))
insert_vals['value_2'] = float(func(metric_vals[1,:]))
insert_vals['name_1'] = compare[1][0]
insert_vals['name_2'] = compare[1][1]
print "%s = %f and %f (twosided_p = %.2f)"%(insert_vals['parameter'], insert_vals['value_1'], insert_vals['value_2'], insert_vals['twosided_p'])
print "INSERT OR REPLACE INTO comparisons ("+",".join(insert_vals.keys()) + ") VALUES (" + ",".join(["?"]*len(insert_vals.values())) + ")"
print insert_vals.values()
c.execute("INSERT OR REPLACE INTO comparisons ("+",".join(insert_vals.keys()) + ") VALUES (" + ",".join(["?"]*len(insert_vals.values())) + ")",
insert_vals.values())
conn.commit()
c.close()
plt.savefig(filename)
def plot_between_within_box_plot(metric, where, filename, exclude):
conn = sqlite3.connect(dbfile)
c = conn.cursor()
metric_vals = []
where_keys = " and ".join([t[0] + "=?" for t in where])
c.execute("SELECT DISTINCT subject_id FROM reliability2010_within_subjects where %s and dice = 0 and distance is NULL ORDER BY subject_id"%(where_keys), tuple([t[1] for t in where]))
exclude = ('subject_id', exclude[1] + [i[0] for i in c.fetchall()])
exclude_clause = "%s not in (%s)"%(exclude[0], ",".join(["'%s'"%s for s in exclude[1]]))
c.execute("SELECT %s FROM reliability2010_within_subjects where %s ORDER BY subject_id"%(metric,where_keys + " and " + exclude_clause), tuple([t[1] for t in where]))
print "SELECT %s FROM reliability2010_within_subjects where %s ORDER BY subject_id"%(metric,where_keys + " and " + exclude_clause), tuple([t[1] for t in where])
res = np.array(c.fetchall(), dtype=np.float)
if len(res) < 2:
return
metric_vals.append(res[:,0])
where_keys = " and ".join([t[0] + "=?" for t in where])
# exclude = []
exclude_str = ""
#
# for key in [t[1] for t in where if t[0] == "contrast_name"]:
# if key.lower().find('finger') != -1 or key.lower().find('foot') != -1:
# exclude = lefties
# break
#
# if exclude:
# #exclude_str = " and (subject_id1 not in (%s) and subject_id2 not in (%s))"%(",".join(["'%s'"%s for s in exclude]), )*2
# exclude_str = " and ((subject_id1 not in (%s) and subject_id2 not in (%s)) or (subject_id1 in (%s) and subject_id2 in (%s)))"%((",".join(["'%s'"%s for s in exclude]), )*4)
if exclude[1]:
exclude_str = " and ((subject_id1 not in (%s) and subject_id2 not in (%s)) or (subject_id1 in (%s) and subject_id2 in (%s)))"%((",".join(["'%s'"%s for s in exclude[1]]), )*4)
c.execute("SELECT %s FROM reliability2010_between_subjects where %s"%(metric,where_keys) + exclude_str, tuple([t[1] for t in where]))
print "SELECT %s FROM reliability2010_between_subjects where %s"%(metric,where_keys) + exclude_str, tuple([t[1] for t in where])
#arr = np.array(c.fetchall())
res = np.array(c.fetchall(), dtype=np.float)
print res.shape
metric_vals.append(res[:,0])
#metric_vals = np.array(metric_vals, dtype=np.float)
conn.commit()
c.close()
fig = plt.figure()
figtitle = ", ".join([t[0] + "=" + str(t[1]) for t in where])
t = fig.text(0.5, 0.95, figtitle,
horizontalalignment='center',
fontproperties=mpl.font_manager.FontProperties(size=16))
ax1 = fig.add_subplot(111)
ax1.boxplot(metric_vals)
ax1.set_xticklabels(["within subjects", "between subjects"])
ax1.set_ylabel(metric + " overlap")
ax1.set_ylim(bottom=-0.1, top=1.1)
if not os.path.exists(os.path.dirname(filename)):
os.makedirs(os.path.dirname(filename))
ax1.text(0.5, 0.90, "onesided_p = %.2f, twosided_p = %.2f"%two_sample(metric_vals[1], metric_vals[0], func=hdmedian),
horizontalalignment='center',
fontproperties=mpl.font_manager.FontProperties(size=16),
transform=ax1.transAxes)
print figtitle
conn = sqlite3.connect(dbfile)
c = conn.cursor()
insert_vals = dict(where)
insert_vals['metric'] = metric
parameters = {'hdmedian': hdmedian,
#'IQR': hdIQR,
'tmean': lambda v:trimr(v, (0.2,0.2)).mean(),
#'winsorized_variance': lambda v:winsorize(v, (0.2,0.2)).var()
}
for parameter,func in parameters.iteritems():
_, insert_vals['twosided_p'], insert_vals['ci_l'], insert_vals['ci_h'] = two_sample(metric_vals[0], metric_vals[1], func = func, ci = True)
insert_vals['parameter'] = parameter
insert_vals['value_1'] = float(func(metric_vals[0]))
insert_vals['value_2'] = float(func(metric_vals[1]))
insert_vals['name_1'] = "within"
insert_vals['name_2'] = "between"
print "%s = %f and %f (twosided_p = %.2f)"%(insert_vals['parameter'], insert_vals['value_1'], insert_vals['value_2'], insert_vals['twosided_p'])
print "INSERT OR REPLACE INTO comparisons ("+",".join(insert_vals.keys()) + ") VALUES (" + ",".join(["?"]*len(insert_vals.values())) + ")"
print insert_vals.values()
c.execute("INSERT OR REPLACE INTO comparisons ("+",".join(insert_vals.keys()) + ") VALUES (" + ",".join(["?"]*len(insert_vals.values())) + ")",
insert_vals.values())
conn.commit()
c.close()
plt.savefig(filename)
