diff options
| -rwxr-xr-x | Wrappers/Python/ccpi/framework/TestData.py | 1 | ||||
| -rw-r--r-- | Wrappers/Python/ccpi/utilities/__init__.py | 0 | ||||
| -rw-r--r-- | Wrappers/Python/ccpi/utilities/display.py | 317 | ||||
| -rw-r--r-- | Wrappers/Python/ccpi/utilities/imagequality.py | 29 | ||||
| -rw-r--r-- | Wrappers/Python/ccpi/utilities/jupyter/__init__.py | 169 | ||||
| -rw-r--r-- | Wrappers/Python/setup.py | 1 |
6 files changed, 516 insertions, 1 deletions
diff --git a/Wrappers/Python/ccpi/framework/TestData.py b/Wrappers/Python/ccpi/framework/TestData.py index 2bb18ce..c035850 100755 --- a/Wrappers/Python/ccpi/framework/TestData.py +++ b/Wrappers/Python/ccpi/framework/TestData.py @@ -86,7 +86,6 @@ class TestData(object): else: tmp = Image.open(os.path.join(self.data_dir, which)) - print (tmp) bands = tmp.getbands() if len(bands) > 1: ig = ImageGeometry(voxel_num_x=size[0], voxel_num_y=size[1], channels=len(bands), diff --git a/Wrappers/Python/ccpi/utilities/__init__.py b/Wrappers/Python/ccpi/utilities/__init__.py new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/Wrappers/Python/ccpi/utilities/__init__.py diff --git a/Wrappers/Python/ccpi/utilities/display.py b/Wrappers/Python/ccpi/utilities/display.py new file mode 100644 index 0000000..cfb20dc --- /dev/null +++ b/Wrappers/Python/ccpi/utilities/display.py @@ -0,0 +1,317 @@ +# -*- coding: utf-8 -*- +# Copyright 2019 Science Technology Facilities Council +# Copyright 2019 University of Manchester +# +# This work is part of the Core Imaging Library developed by Science Technology +# Facilities Council and University of Manchester +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0.txt +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from __future__ import print_function, division +import matplotlib.pyplot as plt +from matplotlib import gridspec +import numpy +from ccpi.framework import ImageGeometry +from mpl_toolkits.axes_grid1 import make_axes_locatable + +def plotter2D(datacontainers, titles=None, fix_range=False, stretch_y=False, cmap='gray', axis_labels=None): + '''plotter2D(datacontainers=[], titles=[], fix_range=False, stretch_y=False, cmap='gray', axes_labels=['X','Y']) + + plots 1 or more 2D plots in an (n x 2) matix + multiple datasets can be passed as a list + + Can take ImageData, AquistionData or numpy.ndarray as input + ''' + if(isinstance(datacontainers, list)) is False: + datacontainers = [datacontainers] + + if titles is not None: + if(isinstance(titles, list)) is False: + titles = [titles] + + + + nplots = len(datacontainers) + rows = int(round((nplots+0.5)/2.0)) + + fig, (ax) = plt.subplots(rows, 2,figsize=(15,15)) + + axes = ax.flatten() + + range_min = float("inf") + range_max = 0 + + if fix_range == True: + for i in range(nplots): + if type(datacontainers[i]) is numpy.ndarray: + dc = datacontainers[i] + else: + dc = datacontainers[i].as_array() + + range_min = min(range_min, numpy.amin(dc)) + range_max = max(range_max, numpy.amax(dc)) + + for i in range(rows*2): + axes[i].set_visible(False) + + for i in range(nplots): + axes[i].set_visible(True) + + if titles is not None: + axes[i].set_title(titles[i]) + + if axis_labels is not None: + axes[i].set_ylabel(axis_labels[1]) + axes[i].set_xlabel(axis_labels[0]) + + if type(datacontainers[i]) is numpy.ndarray: + dc = datacontainers[i] + else: + dc = datacontainers[i].as_array() + + if axis_labels is None: + axes[i].set_ylabel(datacontainers[i].dimension_labels[0]) + axes[i].set_xlabel(datacontainers[i].dimension_labels[1]) + + + sp = axes[i].imshow(dc, cmap=cmap, origin='upper', extent=(0,dc.shape[1],dc.shape[0],0)) + + + im_ratio = dc.shape[0]/dc.shape[1] + + if stretch_y ==True: + axes[i].set_aspect(1/im_ratio) + im_ratio = 1 + + plt.colorbar(sp, ax=axes[i],fraction=0.0467*im_ratio, pad=0.02) + + if fix_range == True: + sp.set_clim(range_min,range_max) + plt.show() + + +def channel_to_energy(channel): + # Convert from channel number to energy using calibration linear fit + m = 0.2786 + c = 0.8575 + # Add on the offset due to using a restricted number of channel (varies based on user choice) + shifted_channel = channel + 100 + energy = (shifted_channel * m) + c + energy = format(energy,".3f") + return energy + + +def show2D(x, title='', **kwargs): + + cmap = kwargs.get('cmap', 'gray') + font_size = kwargs.get('font_size', [12, 12]) + minmax = (kwargs.get('minmax', (x.as_array().min(),x.as_array().max()))) + + # get numpy array + tmp = x.as_array() + + # labels for x, y + labels = kwargs.get('labels', ['x','y']) + + + # defautl figure_size + figure_size = kwargs.get('figure_size', (10,5)) + + # show 2D via plt + fig, ax = plt.subplots(figsize = figure_size) + im = ax.imshow(tmp, cmap = cmap, vmin=min(minmax), vmax=max(minmax)) + ax.set_title(title, fontsize = font_size[0]) + ax.set_xlabel(labels[0], fontsize = font_size[1]) + ax.set_ylabel(labels[1], fontsize = font_size[1]) + divider = make_axes_locatable(ax) + cax1 = divider.append_axes("right", size="5%", pad=0.1) + fig.colorbar(im, ax=ax, cax = cax1) + plt.show() + + + + +def show3D(x, title , **kwargs): + + # show slices for 3D + show_slices = kwargs.get('show_slices', [int(i/2) for i in x.shape]) + + # defautl figure_size + figure_size = kwargs.get('figure_size', (10,5)) + + # font size of title and labels + cmap = kwargs.get('cmap', 'gray') + font_size = kwargs.get('font_size', [12, 12]) + + # Default minmax scaling + minmax = (kwargs.get('minmax', (x.as_array().min(),x.as_array().max()))) + + labels = kwargs.get('labels', ['x','y','z']) + + title_subplot = kwargs.get('title_subplot',['Axial','Coronal','Sagittal']) + + fig, axs = plt.subplots(1, 3, figsize = figure_size) + + tmp = x.as_array() + + im1 = axs[0].imshow(tmp[show_slices[0],:,:], cmap=cmap, vmin=min(minmax), vmax=max(minmax)) + axs[0].set_title(title_subplot[0], fontsize = font_size[0]) + axs[0].set_xlabel(labels[0], fontsize = font_size[1]) + axs[0].set_ylabel(labels[1], fontsize = font_size[1]) + divider = make_axes_locatable(axs[0]) + cax1 = divider.append_axes("right", size="5%", pad=0.1) + fig.colorbar(im1, ax=axs[0], cax = cax1) + + im2 = axs[1].imshow(tmp[:,show_slices[1],:], cmap=cmap, vmin=min(minmax), vmax=max(minmax)) + axs[1].set_title(title_subplot[1], fontsize = font_size[0]) + axs[1].set_xlabel(labels[0], fontsize = font_size[1]) + axs[1].set_ylabel(labels[2], fontsize = font_size[1]) + divider = make_axes_locatable(axs[1]) + cax1 = divider.append_axes("right", size="5%", pad=0.1) + fig.colorbar(im2, ax=axs[1], cax = cax1) + + im3 = axs[2].imshow(tmp[:,:,show_slices[2]], cmap=cmap, vmin=min(minmax), vmax=max(minmax)) + axs[2].set_title(title_subplot[2], fontsize = font_size[0]) + axs[2].set_xlabel(labels[1], fontsize = font_size[1]) + axs[2].set_ylabel(labels[2], fontsize = font_size[1]) + divider = make_axes_locatable(axs[2]) + cax1 = divider.append_axes("right", size="5%", pad=0.1) + fig.colorbar(im3, ax=axs[2], cax = cax1) + + fig.suptitle(title, fontsize = font_size[0]) + plt.tight_layout(h_pad=1) + plt.show() + + +def show2D_channels(x, title, show_channels = [1], **kwargs): + + # defautl figure_size + figure_size = kwargs.get('figure_size', (10,5)) + + # font size of title and labels + cmap = kwargs.get('cmap', 'gray') + font_size = kwargs.get('font_size', [12, 12]) + + labels = kwargs.get('labels', ['x','y']) + + # Default minmax scaling + minmax = (kwargs.get('minmax', (x.as_array().min(),x.as_array().max()))) + + if len(show_channels)==1: + show2D(x.subset(channel=show_channels[0]), title + ' Energy {}'.format(channel_to_energy(show_channels[0])) + " keV", **kwargs) + else: + + fig, axs = plt.subplots(1, len(show_channels), sharey=True, figsize = figure_size) + + for i in range(len(show_channels)): + im = axs[i].imshow(x.subset(channel=show_channels[i]).as_array(), cmap = cmap, vmin=min(minmax), vmax=max(minmax)) + axs[i].set_title('Energy {}'.format(channel_to_energy(show_channels[i])) + "keV", fontsize = font_size[0]) + axs[i].set_xlabel(labels[0], fontsize = font_size[1]) + divider = make_axes_locatable(axs[i]) + cax1 = divider.append_axes("right", size="5%", pad=0.1) + fig.colorbar(im, ax=axs[i], cax = cax1) + axs[0].set_ylabel(labels[1], fontsize = font_size[1]) + fig.suptitle(title, fontsize = font_size[0]) + plt.tight_layout(h_pad=1) + plt.show() + +def show3D_channels(x, title = None, show_channels = 0, **kwargs): + + show3D(x.subset(channel=show_channels), title + ' Energy {}'.format(channel_to_energy(show_channels)) + " keV", **kwargs) + +def show(x, title = None, show_channels = [1], **kwargs): + + sz = len(x.shape) + ch_num = x.geometry.channels + + if ch_num == 1: + + if sz == 2: + show2D(x, title, **kwargs) + elif sz == 3: + show3D(x, title, **kwargs) + + elif ch_num>1: + + if len(x.shape[1:]) == 2: + show2D_channels(x, title, show_channels, **kwargs) + + elif len(x.shape[1:]) == 3: + show3D_channels(x, title, show_channels, **kwargs) + plt.show() + + + + +if __name__ == '__main__': + + from ccpi.framework import TestData, ImageData + import os + import sys + + loader = TestData(data_dir=os.path.join(sys.prefix, 'share','ccpi')) + data = loader.load(TestData.PEPPERS, size=(256,256)) + ig = data.geometry + + show2D(data) + + if False: + + N = 100 + ig2D = ImageGeometry(voxel_num_x=N, voxel_num_y=N) + ig3D = ImageGeometry(voxel_num_x=N, voxel_num_y=N, voxel_num_z=N) + + ch_number = 10 + ig2D_ch = ImageGeometry(voxel_num_x=N, voxel_num_y=N, channels = ch_number) + ig3D_ch = ImageGeometry(voxel_num_x=N, voxel_num_y=N, voxel_num_z=N, channels = ch_number) + + x2D = ig2D.allocate('random_int') + x2D_ch = ig2D_ch.allocate('random_int') + x3D = ig3D.allocate('random_int') + x3D_ch = ig3D_ch.allocate('random_int') + + #%% + ############################################################################### + # test 2D cases + show(x2D) + show(x2D, title = '2D no font') + show(x2D, title = '2D with font', font_size = (50, 30)) + show(x2D, title = '2D with font/fig_size', font_size = (20, 10), figure_size = (10,10)) + show(x2D, title = '2D with font/fig_size', + font_size = (20, 10), + figure_size = (10,10), + labels = ['xxx','yyy']) + ############################################################################### + + + #%% + ############################################################################### + # test 3D cases + show(x3D) + show(x3D, title = '2D no font') + show(x3D, title = '2D with font', font_size = (50, 30)) + show(x3D, title = '2D with font/fig_size', font_size = (20, 20), figure_size = (10,4)) + show(x3D, title = '2D with font/fig_size', + font_size = (20, 10), + figure_size = (10,4), + labels = ['xxx','yyy','zzz']) + ############################################################################### + #%% + + ############################################################################### + # test 2D case + channel + show(x2D_ch, show_channels = [1, 2, 5]) + + ############################################################################### + +
\ No newline at end of file diff --git a/Wrappers/Python/ccpi/utilities/imagequality.py b/Wrappers/Python/ccpi/utilities/imagequality.py new file mode 100644 index 0000000..392eaa7 --- /dev/null +++ b/Wrappers/Python/ccpi/utilities/imagequality.py @@ -0,0 +1,29 @@ +# -*- coding: utf-8 -*- +# Copyright 2019 Science Technology Facilities Council +# Copyright 2019 University of Manchester +# +# This work is part of the Core Imaging Library developed by Science Technology +# Facilities Council and University of Manchester +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0.txt +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from __future__ import print_function, division +import numpy + +def psnr(img1, img2, data_range=1): + mse = numpy.mean( (img1 - img2) ** 2 ) + if mse == 0: + return 1000 + return 20 * numpy.log10(data_range / numpy.sqrt(mse)) + + diff --git a/Wrappers/Python/ccpi/utilities/jupyter/__init__.py b/Wrappers/Python/ccpi/utilities/jupyter/__init__.py new file mode 100644 index 0000000..b87f813 --- /dev/null +++ b/Wrappers/Python/ccpi/utilities/jupyter/__init__.py @@ -0,0 +1,169 @@ +# imports for plotting +from __future__ import print_function, division +from ipywidgets import interact, interactive, fixed, interact_manual +import ipywidgets as widgets +import matplotlib.pyplot as plt +from matplotlib import gridspec +import numpy + +from IPython.display import HTML +import random + + +def display_slice(container, direction, title, cmap, minmax, size, axis_labels): + + + def get_slice_3D(x): + + if direction == 0: + img = container[x] + x_lim = container.shape[2] + y_lim = container.shape[1] + x_label = axis_labels[2] + y_label = axis_labels[1] + + elif direction == 1: + img = container[:,x,:] + x_lim = container.shape[2] + y_lim = container.shape[0] + x_label = axis_labels[2] + y_label = axis_labels[0] + + elif direction == 2: + img = container[:,:,x] + x_lim = container.shape[1] + y_lim = container.shape[0] + x_label = axis_labels[1] + y_label = axis_labels[0] + + if size is None: + fig = plt.figure() + else: + fig = plt.figure(figsize=size) + + if isinstance(title, (list, tuple)): + dtitle = title[x] + else: + dtitle = title + + gs = gridspec.GridSpec(1, 2, figure=fig, width_ratios=(1,.05), height_ratios=(1,)) + # image + ax = fig.add_subplot(gs[0, 0]) + + ax.set_xlabel(x_label) + ax.set_ylabel(y_label) + + aximg = ax.imshow(img, cmap=cmap, origin='upper', extent=(0,x_lim,y_lim,0)) + aximg.set_clim(minmax) + ax.set_title(dtitle + " {}".format(x)) + # colorbar + ax = fig.add_subplot(gs[0, 1]) + plt.colorbar(aximg, cax=ax) + plt.tight_layout() + plt.show(fig) + + return get_slice_3D + + +def islicer(data, direction, title="", slice_number=None, cmap='gray', minmax=None, size=None, axis_labels=None): + + '''Creates an interactive integer slider that slices a 3D volume along direction + + :param data: DataContainer or numpy array + :param direction: slice direction, int, should be 0,1,2 or the axis label + :param title: optional title for the display + :slice_number: int start slice number, optional. If None defaults to center slice + :param cmap: matplotlib color map + :param minmax: colorbar min and max values, defaults to min max of container + :param size: int or tuple specifying the figure size in inch. If int it specifies the width and scales the height keeping the standard matplotlib aspect ratio + ''' + + if axis_labels is None: + if hasattr(data, "dimension_labels"): + axis_labels = [data.dimension_labels[0],data.dimension_labels[1],data.dimension_labels[2]] + else: + axis_labels = ['X', 'Y', 'Z'] + + + if hasattr(data, "as_array"): + container = data.as_array() + + if not isinstance (direction, int): + if direction in data.dimension_labels.values(): + direction = data.get_dimension_axis(direction) + + elif isinstance (data, numpy.ndarray): + container = data + + if slice_number is None: + slice_number = int(data.shape[direction]/2) + + slider = widgets.IntSlider(min=0, max=data.shape[direction]-1, step=1, + value=slice_number, continuous_update=False, description=axis_labels[direction]) + + if minmax is None: + amax = container.max() + amin = container.min() + else: + amin = min(minmax) + amax = max(minmax) + + if isinstance (size, (int, float)): + default_ratio = 6./8. + size = ( size , size * default_ratio ) + + interact(display_slice(container, + direction, + title=title, + cmap=cmap, + minmax=(amin, amax), + size=size, axis_labels=axis_labels), + x=slider); + + return slider + + +def link_islicer(*args): + '''links islicers IntSlider widgets''' + linked = [(widg, 'value') for widg in args] + # link pair-wise + pairs = [(linked[i+1],linked[i]) for i in range(len(linked)-1)] + for pair in pairs: + widgets.link(*pair) + + +# https://stackoverflow.com/questions/31517194/how-to-hide-one-specific-cell-input-or-output-in-ipython-notebook/52664156 + +def hide_toggle(for_next=False): + this_cell = """$('div.cell.code_cell.rendered.selected')""" + next_cell = this_cell + '.next()' + + toggle_text = 'Toggle show/hide' # text shown on toggle link + target_cell = this_cell # target cell to control with toggle + js_hide_current = '' # bit of JS to permanently hide code in current cell (only when toggling next cell) + + if for_next: + target_cell = next_cell + toggle_text += ' next cell' + js_hide_current = this_cell + '.find("div.input").hide();' + + js_f_name = 'code_toggle_{}'.format(str(random.randint(1,2**64))) + + html = """ + <script> + function {f_name}() {{ + {cell_selector}.find('div.input').toggle(); + }} + + {js_hide_current} + </script> + + <a href="javascript:{f_name}()">{toggle_text}</a> + """.format( + f_name=js_f_name, + cell_selector=target_cell, + js_hide_current=js_hide_current, + toggle_text=toggle_text + ) + + return HTML(html)
\ No newline at end of file diff --git a/Wrappers/Python/setup.py b/Wrappers/Python/setup.py index ea6181e..ed2cd25 100644 --- a/Wrappers/Python/setup.py +++ b/Wrappers/Python/setup.py @@ -35,6 +35,7 @@ setup( 'ccpi.optimisation.algorithms', 'ccpi.optimisation.functions', 'ccpi.processors', + 'ccpi.utilities', 'ccpi.utilities.jupyter', 'ccpi.contrib','ccpi.contrib.optimisation', 'ccpi.contrib.optimisation.algorithms'], data_files = [('share/ccpi', ['data/boat.tiff', |