def _run_interface(self, runtime):
self.out_files = []
self.save_subject_list()
self.plot_mask()
self.plot_full_zstat()
self.plot_thresh_zstat()
self.reformat_cluster_table()
self.peaks = peaks = self._load_peaks()
if len(peaks):
self.plot_watershed(peaks)
self.plot_peaks(peaks)
self.plot_boxes(peaks)
else:
fnames = [
nii_to_png(self.inputs.seg_file),
nii_to_png(self.inputs.zstat_thresh_file, "_peaks"),
op.realpath("peak_boxplot.png")
]
self.out_files.extend(fnames)
for name in fnames:
with open(name, "wb"):
pass
return runtime
def _run_interface(self, runtime):
self.out_files = []
self.save_subject_list()
self.plot_mask()
self.plot_full_zstat()
self.plot_thresh_zstat()
self.reformat_cluster_table()
self.peaks = peaks = self._load_peaks()
if len(peaks):
self.plot_watershed(peaks)
self.plot_peaks(peaks)
self.plot_boxes(peaks)
else:
fnames = [nii_to_png(self.inputs.seg_file),
nii_to_png(self.inputs.zstat_thresh_file, "_peaks"),
op.realpath("peak_boxplot.png")]
self.out_files.extend(fnames)
for name in fnames:
with open(name, "wb"):
pass
return runtime
def plot_mask(self):
"""Plot the analysis mask."""
m = Mosaic(stat=self.inputs.mask_file)
m.plot_mask()
out_fname = nii_to_png(self.inputs.mask_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_mask(self):
"""Plot the analysis mask."""
m = Mosaic(stat=self.inputs.mask_file)
m.plot_mask()
out_fname = nii_to_png(self.inputs.mask_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_full_zstat(self):
"""Plot the unthresholded zstat."""
m = Mosaic(stat=self.inputs.zstat_file, mask=self.inputs.mask_file)
m.plot_overlay(cmap="coolwarm", center=True, alpha=.9)
out_fname = nii_to_png(self.inputs.zstat_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_full_zstat(self):
"""Plot the unthresholded zstat."""
m = Mosaic(stat=self.inputs.zstat_file, mask=self.inputs.mask_file)
m.plot_overlay(cmap="coolwarm", center=True, alpha=.9)
out_fname = nii_to_png(self.inputs.zstat_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_tsnr(self):
tsnr = self.inputs.tsnr_file
m = Mosaic(self.mean, tsnr, self.mask, step=1)
m.plot_overlay("cube:1.9:.5", 0, alpha=1, fmt="%d")
png_name = nii_to_png(tsnr)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def plot_residuals(self):
"""Plot the variance of the model residuals across time."""
ss = self.inputs.sigmasquareds_file
m = Mosaic(self.mean, ss, self.mask, step=1)
m.plot_overlay("cube:.8:.2", 0, alpha=.6, fmt="%d")
png_name = nii_to_png(ss)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def plot_residuals(self):
"""Plot the variance of the model residuals across time."""
ss = self.inputs.sigmasquareds_file
m = Mosaic(self.mean, ss, self.mask, step=1)
m.plot_overlay("cube:.8:.2", 0, alpha=.6, fmt="%d")
png_name = nii_to_png(ss)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def plot_thresh_zstat(self):
"""Plot the thresholded zstat."""
m = Mosaic(stat=self.inputs.zstat_thresh_file,
mask=self.inputs.mask_file)
m.plot_activation(pos_cmap="OrRd_r", vfloor=3.3, alpha=.9)
out_fname = nii_to_png(self.inputs.zstat_thresh_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_thresh_zstat(self):
"""Plot the thresholded zstat."""
m = Mosaic(stat=self.inputs.zstat_thresh_file,
mask=self.inputs.mask_file)
m.plot_activation(pos_cmap="OrRd_r", vfloor=3.3, alpha=.9)
out_fname = nii_to_png(self.inputs.zstat_thresh_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_tsnr(self):
tsnr = self.inputs.tsnr_file
m = Mosaic(self.mean, tsnr, self.mask, step=1)
m.plot_overlay("cube:1.9:.5", 0, alpha=1, fmt="%d")
png_name = nii_to_png(tsnr)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def plot_rsquareds(self):
"""Plot the full, main, and confound R squared maps."""
cmaps = ["cube:2:0", "cube:2.6:0", "cube:1.5:0"]
for r2_file, cmap in zip(self.inputs.r2_files, cmaps):
m = Mosaic(self.mean, r2_file, self.mask, step=1)
m.plot_overlay(cmap, 0, alpha=.6)
png_name = nii_to_png(r2_file)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def plot_zstats(self):
"""Plot the positive and negative z stats with a low threshold."""
for z_file in self.inputs.zstat_files:
m = Mosaic(self.mean, z_file, self.mask, step=1)
m.plot_activation(pos_cmap="Reds_r", neg_cmap="Blues",
thresh=1.7, alpha=.85)
png_name = nii_to_png(z_file)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def plot_rsquareds(self):
"""Plot the full, main, and confound R squared maps."""
cmaps = ["cube:2:0", "cube:2.6:0", "cube:1.5:0"]
for r2_file, cmap in zip(self.inputs.r2_files, cmaps):
m = Mosaic(self.mean, r2_file, self.mask, step=1)
m.plot_overlay(cmap, 0, alpha=.6)
png_name = nii_to_png(r2_file)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)
def write_r2_images(self):
"""Show the fixed effects model fit."""
cmaps = ["cube:2:0", "cube:2.6:0"]
for fname, cmap in zip(self.inputs.r2_files, cmaps):
m = Mosaic(self.inputs.anatomy, fname,
self.every_mask, step=self.step)
m.plot_overlay(cmap, 0, alpha=.85)
out_fname = op.abspath(nii_to_png(fname))
self.summary_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_watershed(self, peaks):
"""Plot the watershed segmentation."""
palette = sns.husl_palette(len(peaks))
cmap = mpl.colors.ListedColormap(palette)
m = Mosaic(stat=self.inputs.seg_file, mask=self.inputs.mask_file)
m.plot_overlay(thresh=.5, cmap=cmap, vmin=1, vmax=len(peaks))
out_fname = nii_to_png(self.inputs.seg_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_watershed(self, peaks):
"""Plot the watershed segmentation."""
palette = sns.husl_palette(len(peaks))
cmap = mpl.colors.ListedColormap(palette)
m = Mosaic(stat=self.inputs.seg_file, mask=self.inputs.mask_file)
m.plot_overlay(thresh=.5, cmap=cmap, vmin=1, vmax=len(peaks))
out_fname = nii_to_png(self.inputs.seg_file)
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def write_r2_images(self):
"""Show the fixed effects model fit."""
cmaps = ["cube:2:0", "cube:2.6:0"]
for fname, cmap in zip(self.inputs.r2_files, cmaps):
m = Mosaic(self.inputs.anatomy, fname,
self.every_mask, step=self.step)
m.plot_overlay(cmap, 0, alpha=.85)
out_fname = op.abspath(nii_to_png(fname))
self.summary_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_peaks(self, peaks):
"""Plot the peaks."""
palette = sns.husl_palette(len(peaks))
cmap = mpl.colors.ListedColormap(palette)
disk_img = self._peaks_to_disks(peaks)
m = Mosaic(stat=disk_img, mask=self.inputs.mask_file)
m.plot_overlay(thresh=.5, cmap=cmap, vmin=1, vmax=len(peaks))
out_fname = nii_to_png(self.inputs.zstat_thresh_file, "_peaks")
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_peaks(self, peaks):
"""Plot the peaks."""
palette = sns.husl_palette(len(peaks))
cmap = mpl.colors.ListedColormap(palette)
disk_img = self._peaks_to_disks(peaks)
m = Mosaic(stat=disk_img, mask=self.inputs.mask_file)
m.plot_overlay(thresh=.5, cmap=cmap, vmin=1, vmax=len(peaks))
out_fname = nii_to_png(self.inputs.zstat_thresh_file, "_peaks")
self.out_files.append(out_fname)
m.savefig(out_fname)
m.close()
def plot_zstats(self):
"""Plot the positive and negative z stats with a low threshold."""
for z_file in self.inputs.zstat_files:
m = Mosaic(self.mean, z_file, self.mask, step=1)
m.plot_activation(pos_cmap="Reds_r",
neg_cmap="Blues",
thresh=1.7,
alpha=.85)
png_name = nii_to_png(z_file)
m.savefig(png_name)
m.close()
self.out_files.append(png_name)