def _plotHistogram(self, param=None): md = MetaData() md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM)) x_axis = [] y_axis = [] i = 0 for idx in md: x_axis_ = md.getValue(MDL_X, idx) if i == 0: x0 = x_axis_ elif i == 1: x1 = x_axis_ y_axis_ = md.getValue(MDL_COUNT, idx) i += 1 x_axis.append(x_axis_) y_axis.append(y_axis_) delta = x1 - x0 fig = plt.figure() plt.bar(x_axis, y_axis, width=delta) plt.title("Resolutions Histogram") plt.xlabel("Resolution (A)") plt.ylabel("Counts") return [Plotter(figure2=fig)]
def _plotHistogram(self, fnhist, titlename, xname): md = MetaData() md.read(self.protocol._getPath('extra/' + fnhist)) x_axis = [] y_axis = [] i = 0 for idx in md: x_axis_ = md.getValue(MDL_X, idx) if i == 0: x0 = x_axis_ elif i == 1: x1 = x_axis_ y_axis_ = md.getValue(MDL_COUNT, idx) i += 1 x_axis.append(x_axis_) y_axis.append(y_axis_) delta = x1 - x0 plt.figure() plt.bar(x_axis, y_axis, width=delta) plt.title(titlename + "Histogram") plt.xlabel(xname + "(a.u.)") plt.ylabel("Counts") return plt.show()
def _plotHistogram(self, param=None): md = MetaData() md.read(self.protocol._getPath('extra/hist.xmd')) x_axis = [] y_axis = [] i = 0 for idx in md: x_axis_ = md.getValue(MDL_X, idx) if i==0: x0 = x_axis_ elif i==1: x1 = x_axis_ y_axis_ = md.getValue(MDL_COUNT, idx) i+=1 x_axis.append(x_axis_) y_axis.append(y_axis_) delta = x1-x0 plt.figure() plt.bar(x_axis, y_axis, width = delta) plt.title("Resolutions Histogram") plt.xlabel("Resolution (A)") plt.ylabel("Counts") return plt.show()
def _plotHistogram(self, param=None): md = MetaData() md.read(self.protocol._getPath('extra/hist.xmd')) x_axis = [] y_axis = [] i = 0 for idx in md: x_axis_ = md.getValue(MDL_X, idx) if i == 0: x0 = x_axis_ elif i == 1: x1 = x_axis_ y_axis_ = md.getValue(MDL_COUNT, idx) i += 1 x_axis.append(x_axis_) y_axis.append(y_axis_) delta = x1 - x0 plt.figure() plt.bar(x_axis, y_axis, width=delta) plt.title("Resolutions Histogram") plt.xlabel("Resolution (A)") plt.ylabel("Counts") return plt.show()
def _plotHistogram(self, param=None): md = MetaData() md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM)) x_axis = [] y_axis = [] for idx in md: x_axis_ = md.getValue(MDL_X, idx) y_axis_ = md.getValue(MDL_COUNT, idx) x_axis.append(x_axis_) y_axis.append(y_axis_) plotter = EmPlotter() plotter.createSubPlot("Resolutions Histogram", "Resolution (A)", "# of Counts") barwidth = (x_axis[-1] - x_axis[0]) / len(x_axis) plotter.plotDataBar(x_axis, y_axis, barwidth) return [plotter]
def _showColorSlices(self, fileName, setrangelimits, titleFigure, lowlim, highlim): imageFile = self.protocol._getExtraPath(fileName) img = ImageHandler().read(imageFile) imgData = img.getData() imgData2 = np.ma.masked_where(imgData < 0.001, imgData, copy=True) if setrangelimits is True: fig, im = self._plotVolumeSlices(titleFigure, imgData2, lowlim, highlim, self.getColorMap(), dataAxis=self._getAxis()) else: md = MetaData() md.read(self.protocol._getExtraPath(OUTPUT_THRESHOLDS_FILE)) idx = 1 val1 = md.getValue(MDL_RESOLUTION_FREQ, idx) val2 = md.getValue(MDL_RESOLUTION_FREQ2, idx) if val1 >= val2: max_Res = val1 + 0.01 else: max_Res = val2 # max_Res = np.nanmax(imgData2) min_Res = np.nanmin(imgData2) fig, im = self._plotVolumeSlices(titleFigure, imgData2, min_Res, max_Res, self.getColorMap(), dataAxis=self._getAxis()) cax = fig.add_axes([0.9, 0.1, 0.03, 0.8]) cbar = fig.colorbar(im, cax=cax) cbar.ax.invert_yaxis() return plt.show(fig)