def plot(self):
slope, intercept, rvalue, pvalue, stderr = stats.linregress(
self.xvec, self.yvec)
fig = plt.figure(figsize=(8, 6))
plt.plot(self.xvec, self.yvec, 'o')
# plt.hold(True) # removed intentionally since matplotlib 3.0
a = slope
b = intercept
ax = plt.gca()
# adjust tick size
if self.labelsize is not None:
ax.tick_params(labelsize=self.labelsize)
xlim = ax.get_xlim()
x0 = xlim[0]
x1 = xlim[1]
plt.plot(xlim, [a * x0 + b, a * x1 + b])
if self.title_show_corr:
plt.title(self.title + ' r:{:0.3} p:{:0.3}'.format(rvalue, pvalue))
else:
plt.title(self.title)
plt.xlabel(self.xlabel)
plt.ylabel(self.ylabel)
path.makedirs_file(self.outfilepath)
fig.savefig(self.outfilepath, dpi=300)
plt.close()
def run_mriscan(self, mriscan): src = os.path.join(self.preprocessedFolder, mriscan, 'Filtered_4DVolume.nii') if os.path.isfile(src): dst = os.path.join(self.exportFolder, mriscan, 'pBOLD.nii') path.makedirs_file(dst) shutil.copy2(src, dst) print(mriscan, 'OK') else: print(mriscan, 'not found', src)
def save(self, outfile, addticks=True):
"""Save the attr, can add ticks defined in atlasobj."""
if addticks is False:
save_csvmat(outfile, self.data)
else:
path.makedirs_file(outfile)
with open(outfile, 'w', newline='') as f:
writer = csv.writer(f)
writer.writerow(('Region', 'Value'))
for tick, value in zip(self.atlasobj.ticks, self.data):
writer.writerow((tick, value))
def download(self, urlpath, outfilepath):
"""Blocking download file to outfilepath."""
makedirs_file(outfilepath)
print(urlpath)
r = requests.get(self.full_url(urlpath), stream=True, **self._reqparams)
if r.status_code != 200:
print('Download not allowed or file not exist')
return False
with open(outfilepath, 'wb') as f:
shutil.copyfileobj(r.raw, f)
print('Download OK')
return True
def run_feature(self, feature_name, feature_config):
"""
Export one feature.
feature_name is used in sub-classes
"""
in_file_list, out_file_list = self.get_feature_file_path(feature_config)
for file, filedst in zip(in_file_list, out_file_list):
if not os.path.isfile(file):
print('==Not Exist:', file)
continue
path.makedirs_file(filedst)
#print('Copy:', file, filedst)
shutil.copy2(file, filedst)
def get_file(self, urlpath, localpath):
"""Get file blocking."""
makedirs_file(localpath)
url = self.full_url(urlpath)
r = requests.get(url, stream=True, **self._reqparams)
if r.status_code != 200:
self.error(r, url)
return False
print('Retriving file from {} to {} '.format(url, localpath), end='')
with open(localpath, 'wb') as f:
shutil.copyfileobj(r.raw, f)
print('OK')
return True
def save_list_to_csv(list_data, outfile):
"""
save a list of dicts to a csv file
:param list_data: a list of dicts
:param outfile:
:return:
"""
path.makedirs_file(outfile)
with open(outfile, 'w', newline = '') as f:
writer = csv.DictWriter(f, list_data[0].keys(), delimiter = ',')
writer.writeheader()
for itm in list_data:
writer.writerow(itm)
def save(self, outfile, addticks=True):
"""Save the net, can add ticks defined in atlasobj."""
if addticks is False:
save_csvmat(outfile, self.data)
else:
path.makedirs_file(outfile)
with open(outfile, 'w', newline='') as f:
writer = csv.writer(f)
ticks = self.atlasobj.ticks
firstrow = ['Region']
firstrow.extend(ticks)
writer.writerow(firstrow)
for tick, datarow in zip(self.atlasobj.ticks, self.data):
currow = [tick]
currow.extend(datarow)
writer.writerow(currow)
def plot(self):
plt.figure(figsize=(20, 6))
for attr in self.attrs:
self.count = attr.data.shape[1]
plt.plot(range(1, self.count + 1),
attr.data[self.regionIdx, :],
'.-',
label=attr.scan)
plt.xlim([0, self.count + 1])
plt.xticks(range(1, self.count + 1),
range(1, self.count * self.stepSize, self.stepSize))
plt.grid(True)
plt.legend()
plt.title(self.title, fontsize=20)
path.makedirs_file(self.outfilepath)
plt.savefig(self.outfilepath, dpi=100)
plt.close()
def plot(self, sig_positions=None, stat_list=None, adjust_method=None):
"""
sig_positions should be a vector of 0 and 1, where 1 stands for significance
specify adjust_method as a string ('RSN', 'circos'). Defaults to plot_index
"""
plt.figure(figsize=(20, 6))
plt.xlim(self.xlim)
plt.ylim(self.ylim)
ax = plt.gca()
if stat_list is not None:
# keep significant stats according to sig_positions
stat_list = list(stat_list) # persist zip
new_list = []
for idx, flag in enumerate(sig_positions):
if flag:
stat_list[idx] += (idx, )
new_list.append(stat_list[idx])
stat_list = new_list
if adjust_method == 'RSN':
self.adjust_RSN(ax, sig_positions)
elif adjust_method == 'circos':
self.adjust_circos(ax, sig_positions)
else:
self.adjust_plot_index(sig_positions)
for attr in self.attrs:
plt.plot(range(self.count), attr.data, '.-', label=attr.scan)
plt.xticks(range(self.count), self.plot_ticks, rotation=60)
if sig_positions is not None:
self.add_markers()
plt.grid(True)
plt.legend()
plt.title(self.title, fontsize=20)
path.makedirs_file(self.outfilepath)
plt.savefig(self.outfilepath, dpi=100)
plt.close()
if stat_list is not None:
# add text goes AFTER the image is saved
self.add_text(stat_list)
def plot(self): """Do the plot.""" fig = plt.figure(figsize=(20, 8)) netdata_adjusted = self.atlasobj.adjust_mat_col(self.rowsmat) netdata_adjusted = np.nan_to_num(netdata_adjusted) axim = plt.imshow(netdata_adjusted, interpolation='none', cmap=self.get_cmap(), vmin=self.valuerange[0], vmax=self.valuerange[1]) nrow = self.rowsmat.shape[0] _, ncol = netdata_adjusted.shape ax = fig.gca() ax.set_xticks(range(self.count)) ax.set_xticklabels(self.atlasobj.ticks_adjusted, rotation=90) ax.set_yticks(range(nrow)) ax.set_yticklabels(self.rowsticks) ax.set_xlim(-0.5, ncol-0.5) ax.set_ylim(nrow-0.5, -0.5) #fig.colorbar(axim) plt.title(self.title, fontsize=24) path.makedirs_file(self.outfilepath) plt.savefig(self.outfilepath, dpi=100) plt.close()
def plot(self): """Do the plot.""" fig = plt.figure(figsize=(20, 20)) netdata_adjusted = self.atlasobj.adjust_mat(self.net.data) netdata_adjusted = np.nan_to_num(netdata_adjusted) axim = plt.imshow(netdata_adjusted, interpolation='none', cmap=self.cmap, vmin=self.valuerange[0], vmax=self.valuerange[1]) nrow, ncol = netdata_adjusted.shape ax = fig.gca() ax.set_xlim(-0.5, ncol-0.5) ax.set_ylim(nrow-0.5, -0.5) # set ticks if self.show_ticks: ax.set_xticks(range(self.count)) ax.set_xticklabels(self.atlasobj.ticks_adjusted, rotation=90) ax.set_yticks(range(self.count)) ax.set_yticklabels(self.atlasobj.ticks_adjusted) else: ax.set_xticks([]) ax.set_yticks([]) # set colorbar if self.show_colorbar: cbar = fig.colorbar(axim, fraction=0.046, pad=0.04) # change colorbar ticks font size # see https://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.tick_params # and https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.tick_params.html#matplotlib.axes.Axes.tick_params cbar.ax.tick_params(labelsize = 25, length = 5, width = 5) # save fig plt.title(self.title, fontsize = self.title_font_size) path.makedirs_file(self.outfilepath) plt.savefig(self.outfilepath, dpi = 200) plt.close()
def get_file_progress(self, urlpath, localpath):
"""Get file blocking, with a fancy progress bar."""
makedirs_file(localpath)
url = self.full_url(urlpath)
r = requests.get(url, stream=True, **self._reqparams)
filesize = int(r.headers['content-length'])
if r.status_code != 200:
self.error(r, url)
return False
downloadedsize = 0
progress = 0
print('Retriving file from {} to {} '.format(url, localpath))
with open(localpath, 'wb') as f:
for chunk in r.iter_content(chunk_size=self.CHUNK_SIZE):
if chunk:
downloadedsize = downloadedsize + self.CHUNK_SIZE
newprogress = downloadedsize * self.PROGRESSBAR_LENGTH // filesize
newprogress = newprogress if newprogress < self.PROGRESSBAR_LENGTH else self.PROGRESSBAR_LENGTH
if newprogress != progress:
print('#' * (newprogress - progress), end='')
progress = newprogress
f.write(chunk)
print(' OK')
return True
def write(self, outedgefile): """Write the edge file.""" path.makedirs_file(outedgefile) np.savetxt(outedgefile, self.net.data, delimiter='\t')
def __init__(self, mriscansfolder, outcsvname):
"""Use information from the main mriscan folder, export summary to csv."""
self.mriscansfolder = mriscansfolder
self.outcsvname = outcsvname
path.makedirs_file(self.outcsvname)
def plotRSN(self): """ Similar as plot(), but plot the heatmap according to RSN config file and use black lines to separate RSNs """ fig = plt.figure(figsize=(20, 20)) netdata_adjusted = self.atlasobj.adjust_mat_RSN(self.net.data) netdata_adjusted = np.nan_to_num(netdata_adjusted) axim = plt.imshow(netdata_adjusted, interpolation='none', cmap=self.cmap, vmin=self.valuerange[0], vmax=self.valuerange[1]) nrow, ncol = netdata_adjusted.shape ax = fig.gca() ax.set_xlim(-0.5, ncol-0.5) ax.set_ylim(nrow-0.5, -0.5) # set ticks ticks_adjusted, nodeCount = self.atlasobj.adjust_ticks_RSN() if self.show_ticks: ax.set_xticks(range(self.count)) ax.set_xticklabels(ticks_adjusted, rotation=90) ax.set_yticks(range(self.count)) ax.set_yticklabels(ticks_adjusted) else: ax.set_xticks([]) ax.set_yticks([]) # plot horizontal and vertical lines plotIdx = -0.5 ax.vlines(plotIdx, -0.5, self.count, linewidths = 5) # vposition, start, end ax.hlines(plotIdx, -0.5, self.count, linewidths = 5) # hposition, start, end border = [0] # the border of each RSN, including 0 and max for idx in range(len(nodeCount)): netCount = nodeCount[idx] plotIdx += netCount ax.vlines(plotIdx, -0.5, self.count, linewidths = 5) # vposition, start, end ax.hlines(plotIdx, -0.5, self.count, linewidths = 5) # hposition, start, end border.append(border[-1] + netCount) # add ticks for RSN minorTicks = [] for idx in range(len(border) - 1): minorTicks.append((border[idx] + border[idx+1])/2.0) ax.set_xticks(minorTicks, minor=True) ax.set_yticks(minorTicks, minor=True) ax.tick_params(which="minor", bottom=False, left=False, pad=35, labelsize = 30) # make minor ticks invisible ax.set_xticklabels(self.atlasobj.get_RSN_list(), minor = True) ax.set_yticklabels(self.atlasobj.get_RSN_list(), minor = True) # set colorbar if self.show_colorbar: cbar = fig.colorbar(axim, fraction=0.046, pad=0.04) # change colorbar ticks font size # see https://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.tick_params # and https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.tick_params.html#matplotlib.axes.Axes.tick_params cbar.ax.tick_params(labelsize = 25, length = 5, width = 5) # save fig plt.title(self.title, fontsize = self.title_font_size) path.makedirs_file(self.outfilepath) plt.savefig(self.outfilepath, dpi=200) plt.close()
def write(self, outnodefile): """Write current data to a new node file.""" path.makedirs_file(outnodefile) with open(outnodefile, 'w', newline='') as f: writer = csv.writer(f, delimiter='\t') writer.writerows(self.nodedata)