Exemplo n.º 1
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    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
Exemplo n.º 2
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    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
Exemplo n.º 3
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 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()
Exemplo n.º 4
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 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()
Exemplo n.º 5
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 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()
Exemplo n.º 6
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 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()
Exemplo n.º 7
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    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)
Exemplo n.º 8
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 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)
Exemplo n.º 9
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 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)
Exemplo n.º 10
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 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()
Exemplo n.º 11
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 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()
Exemplo n.º 12
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    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)
Exemplo n.º 13
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 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)
Exemplo n.º 14
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 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)
Exemplo n.º 15
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 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)
Exemplo n.º 16
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 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()
Exemplo n.º 17
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    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()
Exemplo n.º 18
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    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()
Exemplo n.º 19
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 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()
Exemplo n.º 20
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    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()
Exemplo n.º 21
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    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()
Exemplo n.º 22
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 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)