I have a code which resizes an image and gets its entropy.
Resize works correctly, but I cannot do something with quantiz.
This function throws
Error using quantiz (line 31)
The input signal must be a real vector.
Error. How to fix it?(GrayImage is 2D array with values from 0 to 255)
normalImage = imread("porshe.bmp");
grayImage = rgb2gray(normalImage);
width = 750;
heigth = 500;
ebase = entropy(grayImage);
resizedImage2 = imresize(grayImage,0.5);
resizedImage4 = imresize(grayImage,0.25);
er2 = entropy(resizedImage2);
er4 = entropy(resizedImage4);
quantizImage8 = quantiz(grayImage,8);
quantizImage16 = quantiz(grayImage,16);
quantizImage64 = quantiz(grayImage,64);
imshow(quantizImage64)
I have a vector shapefile which is in unit of 'Meter' presenting boundary of overall Germany. I am converting it into raster format based on each pixel representing 300 Meters respectively. After conversion I accessed inmage information using imfinfo() in matlab. However the result is giving me the unit value is in "Inches" I am quite confused at the moment and do not know what to do to convert inches to meters as a pixel size unit. Would you please give me some idea?
`% Code
R6 = shaperead('B6c.shp');
%Nord
XN6 = double(R6(4).X); YN6 = double(R6(4).Y);
XN6min = min(XN6(XN6>0)); XNmax = max(XN6);
YN6min = min(YN6(YN6>0)); YNmax = max(YN6);
%Bayern
XB6 = double(R6(7).X); YB6 = double(R6(7).Y);
XB6min = min(XB6(XB6>0)); XB6max = max(XB6);
YB6min = min(YB6(YB6>0)); YB6max = max(YB6);
%Schleswig-Holstein
XSH6 = double(R6(9).X); YSH6 = double(R6(9).Y);
XSH6min = min(XSH6(XSH6>0)); XSH6max = max(XSH6);
YSH6min = min(YSH6(YSH6>0)); YSH6max = max(YSH6);
%Sachsen
XS6 = double(R6(6).X); YS6 = double(R6(6).Y);
XS6min = min(XS6(XS6>0)); XS6max = max(XS6);
YS6min = min(YS6(YS6>0)); YS6max = max(YS6);
dx = round(XS6max-XN6min);
dy = round(YSH6max-YB6min);
M = round((dx)/300);enter code here N = round((dy)/300);
A6 = zeros(M,N); %initiating image matrix based on 4 limiting States
%transformation from world to pixel coordinates
xpix_bw =(((XBW-XN6min)*M)/dx)';
ypix_bw =(((YBW-YB6min)*N)/dy)';
xbw6=round(xpix_bw); xbw6=xbw6(~isnan(xbw6));
ybw6=round(ypix_bw); ybw6=ybw6(~isnan(ybw6));
%line drawing
for i=1:1:length(xbw6)-1
j=i+1;
x1=xbw6(i); x2=xbw6(j); y1=ybw6(i); y2=ybw6(j);
nn=atan2((y2-y1),(x2-x1)); % azimuthal angle
if x2==x1
l=abs(y2-y1);
else
l = round((x2-x1)/cos(nn)); % horizontal distance
end
xx=zeros(l,1); %empty column
yy=zeros(l,1); %empty column
% creating line along slope distance
for i=1:1:l
xx(i)=round(x1+cos(nn)*i);
yy(i)=round(y1+sin(nn)*i);
A6(xx(i)+1,yy(i)+1) = 256;
end
end
imwrite(A6, 'Untitled_0506_300.tif','Resolution', 300);`
I'm a new ILNumerics Visualization Engine user and I'm still coming up to speed on how to use it well. I've searched extensively for how to update the z-values of an ILSurface and read the posts, but I'm still not clear on how to do this.
I'm able to generate a surface and set up a camera to view it (Hamyo Kutschbach told me that's the best way to ensure that the aspect ratios of the surface don't change when rotating the surface, which is important in my application). Here's the code that displays a sin(x)/x function:
// Generate the data
ILArray<double> z = SincFunc(rows, cols, 10, 50);
ILArray<double> x = new double[cols];
ILArray<double> y = new double[rows];
for (int i = 0; i < cols; i++)
x[i] = (double)i;
for (int i = 0; i < rows; i++)
y[i] = (double)i;
// create the scene
scene = new ILScene();
pointCloudSurface = new ILSurface(z, x, y)
{
Colormap = Colormaps.Jet,
UseLighting = true,
Wireframe = { Visible = false },
Children = { new ILColorbar()
{
Height = 0.5f,
Location = new PointF(0.95f, 0.05f),
Children = { new ILLabel("microns") { Position = new Vector3(0.5,1,0), Anchor = new PointF(0.5f,0) } } }
},
Alpha = 1.0f
};
// Configure the surface and display it
scene.Camera.Add(pointCloudSurface);
scene.Camera.Position = new Vector3(50, 50, 700);
scene.Camera.LookAt = new Vector3(50, 50, 0);
scene.Camera.Top = new Vector3(0, 0, 700);
scene.Camera.Projection = Projection.Perspective;
scene.Camera.ZNear = 1.0f;
scene.Camera.ZFar = 0.0f;
scene.Camera.Top = new Vector3(1, 0, 0);
// Turn off the Powered by ILNumerics label
scene.Screen.First<ILLabel>().Visible = false;
ilPanel1.Scene = scene;
ilPanel1.Configure();
ilPanel1.Refresh();
And it works well. So now I want to change the z-values and update the plot without closing ilPanel1 because this plot is embedded in a Windows Form. Advice would be appreciated! Hopefully other newbies will find this post useful as well.
After further rummaging around, I came across a method, UpdateColormapped(), that does the trick. It's placed near the end of the code above like this:
scene.Camera.First<ILSurface>().UpdateColormapped(z);
ilPanel1.Scene = scene;
ilPanel1.Configure();
ilPanel1.Refresh();
It can be found in the API documentation here: UpdateColormapped()
It can also change the x and y data and perform other mods, but it requires that the z data be a float array, so if you're working double precision, you'll have to take the appropriate steps to get it into a float array.
Does bokeh have a simple way to plot the colorbar for a heatmap?
In this example it would be a strip illustrating how colors correspond to values.
In matlab, its called a 'colorbar' and looks like this:
UPDATE: This is now much easier: see
http://docs.bokeh.org/en/latest/docs/user_guide/annotations.html#color-bars
I'm afraid I don't have a great answer, this should be easier in Bokeh. But I have done something like this manually before.
Because I often want these off my plot, I make a new plot, and then assemble it together with something like hplot or gridplot.
There is an example of this here: https://github.com/birdsarah/pycon_2015_bokeh_talk/blob/master/washmap/washmap/water_map.py#L179
In your case, the plot should be pretty straight forward. If you made a datasource like this:
| value | color
| 1 | blue
.....
| 9 | red
Then you could do something like:
legend = figure(tools=None)
legend.toolbar_location=None
legend.rect(x=0.5, y='value', fill_color='color', width=1, height=1, source=source)
layout = hplot(main, legend)
show(legend)
However, this does rely on you knowing the colors that your values correspond to. You can pass a palette to your heatmap chart call - as shown here: http://docs.bokeh.org/en/latest/docs/gallery/cat_heatmap_chart.html so then you would be able to use that to construct the new data source from that.
I'm pretty sure there's at least one open issue around color maps. I know I just added one for off-plot legends.
Since other answers here seem very complicated, here an easily understandable piece of code that generates a colorbar on a bokeh heatmap.
import numpy as np
from bokeh.plotting import figure, show
from bokeh.models import LinearColorMapper, BasicTicker, ColorBar
data = np.random.rand(10,10)
color_mapper = LinearColorMapper(palette="Viridis256", low=0, high=1)
plot = figure(x_range=(0,1), y_range=(0,1))
plot.image(image=[data], color_mapper=color_mapper,
dh=[1.0], dw=[1.0], x=[0], y=[0])
color_bar = ColorBar(color_mapper=color_mapper, ticker= BasicTicker(),
location=(0,0))
plot.add_layout(color_bar, 'right')
show(plot)
Since the 0.12.3 version Bokeh has the ColorBar.
This documentation was very useful to me:
http://docs.bokeh.org/en/dev/docs/user_guide/annotations.html#color-bars
To do this I did the same as #birdsarah. As an extra tip though if you use the rect method as your colour map, then use the rect method once again in the colour bar and use the same source. The end result is that you can select sections of the colour bar and it also selects in your plot.
Try it out:
http://simonbiggs.github.io/electronfactors
Here is some code loosely based on birdsarah's response for generating a colorbar:
def generate_colorbar(palette, low=0, high=15, plot_height = 100, plot_width = 500, orientation = 'h'):
y = np.linspace(low,high,len(palette))
dy = y[1]-y[0]
if orientation.lower()=='v':
fig = bp.figure(tools="", x_range = [0, 1], y_range = [low, high], plot_width = plot_width, plot_height=plot_height)
fig.toolbar_location=None
fig.xaxis.visible = None
fig.rect(x=0.5, y=y, color=palette, width=1, height = dy)
elif orientation.lower()=='h':
fig = bp.figure(tools="", y_range = [0, 1], x_range = [low, high],plot_width = plot_width, plot_height=plot_height)
fig.toolbar_location=None
fig.yaxis.visible = None
fig.rect(x=y, y=0.5, color=palette, width=dy, height = 1)
return fig
Also, if you are interested in emulating matplot lib colormaps, try using this:
import matplotlib as mpl
def return_bokeh_colormap(name):
cm = mpl.cm.get_cmap(name)
colormap = [rgb_to_hex(tuple((np.array(cm(x))*255).astype(np.int))) for x in range(0,cm.N)]
return colormap
def rgb_to_hex(rgb):
return '#%02x%02x%02x' % rgb[0:3]
This is high on my wish list as well. It would also need to automatically adjust the range if the plotted data changed (e.g. moving through one dimension of a 3D data set). The code below does something which people might find useful. The trick is to add an extra axis to the colourbar which you can control through a data source when the data changes.
import numpy
from bokeh.plotting import Figure
from bokeh.models import ColumnDataSource, Plot, LinearAxis
from bokeh.models.mappers import LinearColorMapper
from bokeh.models.ranges import Range1d
from bokeh.models.widgets import Slider
from bokeh.models.widgets.layouts import VBox
from bokeh.core.properties import Instance
from bokeh.palettes import RdYlBu11
from bokeh.io import curdoc
class Colourbar(VBox):
plot = Instance(Plot)
cbar = Instance(Plot)
power = Instance(Slider)
datasrc = Instance(ColumnDataSource)
cbarrange = Instance(ColumnDataSource)
cmap = Instance(LinearColorMapper)
def __init__(self):
self.__view_model__ = "VBox"
self.__subtype__ = "MyApp"
super(Colourbar,self).__init__()
numslices = 6
x = numpy.linspace(1,2,11)
y = numpy.linspace(2,4,21)
Z = numpy.ndarray([numslices,y.size,x.size])
for i in range(numslices):
for j in range(y.size):
for k in range(x.size):
Z[i,j,k] = (y[j]*x[k])**(i+1) + y[j]*x[k]
self.power = Slider(title = 'Power',name = 'Power',start = 1,end = numslices,step = 1,
value = round(numslices/2))
self.power.on_change('value',self.inputchange)
z = Z[self.power.value]
self.datasrc = ColumnDataSource(data={'x':x,'y':y,'z':[z],'Z':Z})
self.cmap = LinearColorMapper(palette = RdYlBu11)
r = Range1d(start = z.min(),end = z.max())
self.cbarrange = ColumnDataSource(data = {'range':[r]})
self.plot = Figure(title="Colourmap plot",x_axis_label = 'x',y_axis_label = 'y',
x_range = [x[0],x[-1]],y_range=[y[0],y[-1]],
plot_height = 500,plot_width = 500)
dx = x[1] - x[0]
dy = y[1] - y[0]
self.plot.image('z',source = self.datasrc,x = x[0]-dx/2, y = y[0]-dy/2,
dw = [x[-1]-x[0]+dx],dh = [y[-1]-y[0]+dy],
color_mapper = self.cmap)
self.generate_colorbar()
self.children.append(self.power)
self.children.append(self.plot)
self.children.append(self.cbar)
def generate_colorbar(self,cbarlength = 500,cbarwidth = 50):
pal = RdYlBu11
minVal = self.datasrc.data['z'][0].min()
maxVal = self.datasrc.data['z'][0].max()
vals = numpy.linspace(minVal,maxVal,len(pal))
self.cbar = Figure(tools = "",x_range = [minVal,maxVal],y_range = [0,1],
plot_width = cbarlength,plot_height = cbarwidth)
self.cbar.toolbar_location = None
self.cbar.min_border_left = 10
self.cbar.min_border_right = 10
self.cbar.min_border_top = 0
self.cbar.min_border_bottom = 0
self.cbar.xaxis.visible = None
self.cbar.yaxis.visible = None
self.cbar.extra_x_ranges = {'xrange':self.cbarrange.data['range'][0]}
self.cbar.add_layout(LinearAxis(x_range_name = 'xrange'),'below')
for r in self.cbar.renderers:
if type(r).__name__ == 'Grid':
r.grid_line_color = None
self.cbar.rect(x = vals,y = 0.5,color = pal,width = vals[1]-vals[0],height = 1)
def updatez(self):
data = self.datasrc.data
newdata = data
z = data['z']
z[0] = data['Z'][self.power.value - 1]
newdata['z'] = z
self.datasrc.trigger('data',data,newdata)
def updatecbar(self):
minVal = self.datasrc.data['z'][0].min()
maxVal = self.datasrc.data['z'][0].max()
self.cbarrange.data['range'][0].start = minVal
self.cbarrange.data['range'][0].end = maxVal
def inputchange(self,attrname,old,new):
self.updatez()
self.updatecbar()
curdoc().add_root(Colourbar())
I’m having 2 problems with a simple XYSeries line graph.
When the absolute value of the difference between the last plotted point and the next plotted point is less than 11 the label on the next plotted point goes missing. I want all the labels to display.
I have some (not all) missing vertical grid lines and don’t see why. I want a vertical grid line for every XY coordinate.
Thanks for the help. Here's the code.
String glucoseLegendText = getString(R.string.glucose_legend_text);
XYSeries series = new XYSeries(glucoseLegendText);
datasource = new HistoryDataSource(this);
datasource.open();
Cursor c = datasource.getQuery();
c.moveToFirst();
int cnt = c.getCount();
int minValue = 0;
int maxValue = 0;
for (int i = 0; i < cnt; i++) {
int glucoseValue = c.getInt(2);
series.add(i, glucoseValue);
if (i == 0 || glucoseValue < minValue)
minValue = glucoseValue;
if (glucoseValue > maxValue)
maxValue = glucoseValue;
c.moveToNext();
}
datasource.close();
XYMultipleSeriesDataset dataset = new XYMultipleSeriesDataset();
dataset.addSeries(series);
XYSeriesRenderer renderer = new XYSeriesRenderer();
renderer.setColor(Color.BLUE);
renderer.setPointStyle(PointStyle.CIRCLE);
renderer.setFillPoints(true);
renderer.setLineWidth(3);
renderer.setDisplayChartValues(true);
renderer.setChartValuesTextSize(15);
renderer.setChartValuesTextAlign(Align.LEFT);
XYMultipleSeriesRenderer mRenderer = new XYMultipleSeriesRenderer();
mRenderer.addSeriesRenderer(renderer);
mRenderer.setShowGrid(true);
mRenderer.setGridColor(Color.BLACK);
mRenderer.setXLabels(cnt); // to control number of grid lines
mRenderer.setYLabels(cnt); // to control number of grid lines
mRenderer.setXLabelsColor(Color.YELLOW);
mRenderer.setPointSize(5);
mRenderer.setYLabelsAlign(Align.RIGHT);
mRenderer.setLegendTextSize(15);
mRenderer.setZoomButtonsVisible(true);
mRenderer.setYAxisMin(minValue - 2); // buffer bottom
mRenderer.setYAxisMax(maxValue + 3); // buffer top
// Populate the X labels with the dates and times
c.moveToFirst();
for (int d = 0; d < cnt; d++) {
timeStamp = c.getString(1);
date = timeStamp.substring(0, 5);
time = timeStamp.substring(9, 14);
if (date.equals(dateLast)) {
mRenderer.addXTextLabel(d, "\n" + time);
} else
mRenderer.addXTextLabel(d, "\n" + time + "\n" + date);
dateLast = date;
c.moveToNext();
}
c.close();
GraphicalView gview = ChartFactory.getTimeChartView(this, dataset,
mRenderer, "");
LinearLayout layout = (LinearLayout) findViewById(R.id.Chart);
layout.addView(gview);
For the first question, you can control the labels display using
renderer.setXLabels(approximateNumberOfLabels);
For the second question, the grid lines are displayed along the labels.