Re: [Numpy-discussion] display numpy array as image
Hi Zach
Attached is some code for removing radial distortion from images. It
shows how to draw lines based on user input using matplotlib. It is
not suited for a big application, but useful for demonstrations.
Try it on
http://mentat.za.net/results/window.jpg
Regards
Stéfan
On Thu, Nov 29, 2007 at 11:59:05PM -0500, Zachary Pincus wrote:
Thanks for the suggestions, everyone! All very informative and most
helpful.
For what it's worth, here's my application: I'm building a tool for
image processing which needs some manual input in a few places (e.g.
user draws a few lines). The images are greyscale images with 12-14
bits of dynamic range (from a microscope), so I need to have some
basic brightness/contrast/gamma controls, as well as allowing basic
drawing on the image to get the needed user input. It looks like GL
or wx will be best suited here, I think? (I presume that python/numpy/
[GL|wx] can keep up with things like dragging a slider to change
brightness/contrast/other LUT changes, as long as I code reasonably.)
Anyhow, thanks for all the input,
Zach
Remove radial distortion.
Author: Stefan van der Walt
Date: 2006
import scipy as S
import scipy.optimize
import scipy.ndimage
import pylab as P
import numpy as N
import math
import sys
class RadialDistortionInterface:
Mouse interaction interface for radial distortion removal.
def __init__(self, img):
imshape = img.shape
self.figure = P.imshow(img, extent=(0,imshape[1],imshape[0],0))
P.title('Removal of radial distortion')
P.xlabel('Select sets of three points with left mouse button,\nclick right button to process.')
P.connect('button_press_event', self.button_press)
P.connect('motion_notify_event', self.mouse_move)
self.img = N.atleast_3d(img)
self.points = []
self.centre = ((N.array(self.img.shape)-1)/2.)[:2][::-1]
self.height = imshape[0]
self.width = imshape[1]
self.make_cursorline()
self.figure.axes.set_autoscale_on(False)
P.show()
P.close()
def make_cursorline(self):
self.cursorline, = P.plot([0],[0],'r:+',
linewidth=2,markersize=15,markeredgecolor='b')
def button_press(self,event):
Register mouse clicks.
if (event.button == 1 and event.xdata and event.ydata):
self.points.append((event.xdata,event.ydata))
print Coordinate entered: (%f,%f) % (event.xdata, event.ydata)
if len(self.points) % 3 == 0:
P.gca().lines.append(self.cursorline)
self.make_cursorline()
if (event.button != 1 and len(self.points) = 3):
print Removing distortion...
P.gca().lines = []
P.draw()
self.remove_distortion()
self.points = []
def mouse_move(self,event):
Handle cursor drawing.
pt_sets,pts_last_set = divmod(len(self.points),3)
pts = N.zeros((3,2))
if pts_last_set 0:
# Line follows up to 3 clicked points:
pts[:pts_last_set] = self.points[-pts_last_set:]
# The last point of the line follows the mouse cursor
pts[pts_last_set:] = [event.xdata,event.ydata]
self.cursorline.set_data(pts[:,0],pts[:,1])
P.draw()
def stackcopy(self,a,b):
a[:,:,0] = a[:,:,1] = ... = b
if a.ndim == 3:
a.transpose().swapaxes(1,2)[:] = b
else:
a[:] = b
def remove_distortion(self,reshape=True):
def radii_tf(x,y,p):
Radially distort coordinates.
Given a coordinate (x,y), apply the radial distortion defined by
L(r) = 1 + p[2]r + p[3]r^2 + p[4]r^3
where
r = sqrt((x-p[0])^2 + (y-p[1])^2)
so that
x' = L(r)x and y' = L(r)y
Inputs:
x,y -- Coordinate
p[0],p[1] -- Distortion centre
p[2],p[3],p[4] -- Distortion parameters
Outputs:
x', y'
x = x - p[0]
y = y - p[1]
r = N.sqrt(x**2 + y**2)
f = 1 + p[2]*r + p[3]*r**2 + p[4]*r**3
return x*f + p[0], y*f + p[1]
def height_difference(p):
Measure deviation of distorted data points from straight line.
out = 0
for sets in 3*N.arange(len(self.points)/3):
pts = N.array(self.points[sets:sets+3])
x,y = radii_tf(pts[:,0],pts[:,1],p)
# Find point on line (point0 - point2) closest to point1 (midpoint)
u0 = ((x[0]-x[2])**2 + (y[0]-y[2])**2)
if u0
Re: [Numpy-discussion] display numpy array as image
Hi Stéfan, Thanks -- I hadn't realized matplotlib's user-interaction abilities were that sophisticated! I'll definitely give that route a shot. Zach On Dec 3, 2007, at 9:46 AM, Stefan van der Walt wrote: Hi Zach Attached is some code for removing radial distortion from images. It shows how to draw lines based on user input using matplotlib. It is not suited for a big application, but useful for demonstrations. Try it on http://mentat.za.net/results/window.jpg Regards Stéfan On Thu, Nov 29, 2007 at 11:59:05PM -0500, Zachary Pincus wrote: Thanks for the suggestions, everyone! All very informative and most helpful. For what it's worth, here's my application: I'm building a tool for image processing which needs some manual input in a few places (e.g. user draws a few lines). The images are greyscale images with 12-14 bits of dynamic range (from a microscope), so I need to have some basic brightness/contrast/gamma controls, as well as allowing basic drawing on the image to get the needed user input. It looks like GL or wx will be best suited here, I think? (I presume that python/ numpy/ [GL|wx] can keep up with things like dragging a slider to change brightness/contrast/other LUT changes, as long as I code reasonably.) Anyhow, thanks for all the input, Zachradial.py ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image (Giorgio F. Gilestro)
On Freitag 30 November 2007, Joe Harrington wrote: I was misinformed about the status of numdisplay's pages. The package is available as both part of stsci_python and independently, and its (up-to-date) home page is here: http://stsdas.stsci.edu/numdisplay/ I had a look at ds9/numdisplay, and as a summary, I found a nice viewer for scalar images with colormap support, and x/y projections. What I missed though is the display of RGB images. It looks as if ds9 was capable of doing so (I could add frames of RGB type), but I did not find a way to feed them with data. numdisplay.display(myarray) seems to only support 2D-arrays. Ciao, / /.o. /--/ ..o / / ANS ooo signature.asc Description: This is a digitally signed message part. ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image (Giorgio F. Gilestro)
I was misinformed about the status of numdisplay's pages. The package is available as both part of stsci_python and independently, and its (up-to-date) home page is here: http://stsdas.stsci.edu/numdisplay/ Googling numdisplay finds that page. My apologies to those inconvenienced by my prior post. Note that there is practical documentation and examples of how to use it for astronomical image display in the Data Analysis Tutorial: http://www.scipy.org/wikis/topical_software/Tutorial --jh-- ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image
I am not sure I got what you mean but I am using PIL to convert arrays to images and viceversa see http://mail.python.org/pipermail/image-sig/2006-September/004099.html I embed bmps using wxpython. Zachary Pincus wrote: Hello all, I'm curious if people have experience with / preferences for how to display a numpy array onscreen as an image. Pyglet looks relatively easy -- you can feed an image buffer object with a string or a ctypes pointer. I presume getting a string from an array is plenty fast, but the ctypes pointer option is intriguing as it allows for dealing with simple strided arrays (the image objects allow for an arbitrary number of bytes between rows). Is it possible to get a ctypes pointer to the beginning of the array buffer from numpy without too much ugliness? wxPython looks pretty easy too, as there are facilities for getting pixels from a buffer. Does anyone have any experience with these? Are there ways of allowing a numpy array and a wxPython image to point to the same memory? Anyhow, these are specific questions, but I'd also appreciate any general thoughts about good approaches for getting pixels from numpy arrays onscreen. Thanks, Zach ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion -- [EMAIL PROTECTED] http://www.cafelamarck.it ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image
On 30/11/2007, Zachary Pincus [EMAIL PROTECTED] wrote: Hello all, I'm curious if people have experience with / preferences for how to display a numpy array onscreen as an image. I'm not sure if you're after anything specific, but a very convenient way to show 2-D arrays on screen is matplotlib (mpl), which is the recommended graphical interface to numpy. With the pylab interface to mpl, the command is as simple as pylab.imshow(arr) or pylab.matshow(arr) for slightly different axis behaviour. Angus. -- AJC McMorland, PhD Student Physiology, University of Auckland ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image
On Nov 29, 2007 2:32 PM, Zachary Pincus [EMAIL PROTECTED] wrote: Hello all, I'm curious if people have experience with / preferences for how to display a numpy array onscreen as an image. Pyglet looks relatively easy -- you can feed an image buffer object with a string or a ctypes pointer. I presume getting a string from an array is plenty fast, but the ctypes pointer option is intriguing as it allows for dealing with simple strided arrays (the image objects allow for an arbitrary number of bytes between rows). Is it possible to get a ctypes pointer to the beginning of the array buffer from numpy without too much ugliness? wxPython looks pretty easy too, as there are facilities for getting pixels from a buffer. Does anyone have any experience with these? Are there ways of allowing a numpy array and a wxPython image to point to the same memory? Anyhow, these are specific questions, but I'd also appreciate any general thoughts about good approaches for getting pixels from numpy arrays onscreen. Thanks, Zach ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion Have you tried the matplotlib/pylab module? It has pretty simple ways of doing what you're thinking of if I'm understanding your intent correctly.. Josh ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image
Zachary Pincus wrote:
wxPython looks pretty easy too, as there are facilities for getting
pixels from a buffer. Does anyone have any experience with these?
some.
Are
there ways of allowing a numpy array and a wxPython image to point to
the same memory?
yup. You can build a wxImage from a buffer, and numpy provides a buffer
interface, so they end up with them sharing the same memory, as long as
your numpy array is contiguous 24 rgb.
I've enclosed a sample that generates a wx.Image from a numpy array,
then every time you push the button, the array is altered in-place, and
you can see the image change.
( think you need at least wxPython 2.8 for this to work)
-Chris
--
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Oceanographer
Emergency Response Division
NOAA/NOS/ORR(206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
[EMAIL PROTECTED]
#!/usr/bin/env python2.5
a small test of initializing a wxImage from a numpy array
import wx
import numpy as N
import numpy.random as rand
class ImagePanel(wx.Panel):
A very simple panel for displaying a wx.Image
def __init__(self, image, *args, **kwargs):
wx.Panel.__init__(self, *args, **kwargs)
self.image = image
self.Bind(wx.EVT_PAINT, self.OnPaint)
def OnPaint(self, event):
dc = wx.PaintDC(self)
dc.DrawBitmap(wx.BitmapFromImage(self.image), 0, 0)
class DemoFrame(wx.Frame):
This window displays a button
def __init__(self, title = Micro App):
wx.Frame.__init__(self, None , -1, title)
MenuBar = wx.MenuBar()
FileMenu = wx.Menu()
item = FileMenu.Append(wx.ID_ANY, text = Open)
self.Bind(wx.EVT_MENU, self.OnOpen, item)
item = FileMenu.Append(wx.ID_PREFERENCES, text = Preferences)
self.Bind(wx.EVT_MENU, self.OnPrefs, item)
item = FileMenu.Append(wx.ID_EXIT, text = Exit)
self.Bind(wx.EVT_MENU, self.OnQuit, item)
MenuBar.Append(FileMenu, File)
HelpMenu = wx.Menu()
item = HelpMenu.Append(wx.ID_HELP, Test Help,
Help for this simple test)
self.Bind(wx.EVT_MENU, self.OnHelp, item)
## this gets put in the App menu on OS-X
item = HelpMenu.Append(wx.ID_ABOUT, About,
More information About this program)
self.Bind(wx.EVT_MENU, self.OnAbout, item)
MenuBar.Append(HelpMenu, Help)
self.SetMenuBar(MenuBar)
btn = wx.Button(self, label = NewImage)
btn.Bind(wx.EVT_BUTTON, self.OnNewImage )
self.Bind(wx.EVT_CLOSE, self.OnQuit)
##Create numpy array, and image from it
w = h = 200
self.array = rand.randint(0, 255, (3, w, h)).astype('uint8')
print self.array
image = wx.ImageFromBuffer(w, h, self.array)
#image = wx.Image(Images/cute_close_up.jpg)
self.Panel = ImagePanel(image, self)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(btn, 0, wx.ALIGN_CENTER|wx.ALL, 5)
sizer.Add(self.Panel, 1, wx.GROW)
self.SetSizer(sizer)
def OnNewImage(self, event=None):
create a new image by changing underlying numpy array
self.array *= 1.2
self.Panel.Refresh()
def OnQuit(self,Event):
self.Destroy()
def OnAbout(self, event):
dlg = wx.MessageDialog(self, This is a small program to test\n
the use of menus on Mac, etc.\n,
About Me, wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def OnHelp(self, event):
dlg = wx.MessageDialog(self, This would be help\n
If there was any\n,
Test Help, wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def OnOpen(self, event):
dlg = wx.MessageDialog(self, This would be an open Dialog\n
If there was anything to open\n,
Open File, wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
def OnPrefs(self, event):
dlg = wx.MessageDialog(self, This would be an preferences Dialog\n
If there were any preferences to set.\n,
Preferences, wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
app = wx.App(False)
frame = DemoFrame()
frame.Show()
app.MainLoop()
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Re: [Numpy-discussion] display numpy array as image
Zachary Pincus wrote: Hello all, I'm curious if people have experience with / preferences for how to display a numpy array onscreen as an image. Pyglet looks relatively easy -- you can feed an image buffer object with a string or a ctypes pointer. I presume getting a string from an array is plenty fast, but the ctypes pointer option is intriguing as it allows for dealing with simple strided arrays (the image objects allow for an arbitrary number of bytes between rows). Is it possible to get a ctypes pointer to the beginning of the array buffer from numpy without too much ugliness? In [16]: from numpy import * In [17]: a = arange(10) In [18]: dir(a.ctypes) Out[18]: ['__class__', '__delattr__', '__dict__', '__doc__', '__getattribute__', '__hash__', '__init__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__', '__weakref__', '_arr', '_as_parameter_', '_ctypes', '_data', '_zerod', 'data', 'data_as', 'get_as_parameter', 'get_data', 'get_shape', 'get_strides', 'shape', 'shape_as', 'strides', 'strides_as'] In [22]: import ctypes In [24]: a.ctypes.data_as(ctypes.POINTER(ctypes.c_long)) Out[24]: ctypes.LP_c_long object at 0x1b353a0 In [25]: a.ctypes.get_shape() Out[25]: numpy.core._internal.c_long_Array_1 object at 0x1c096c0 In [26]: a.ctypes.get_strides() Out[26]: numpy.core._internal.c_long_Array_1 object at 0x1c09710 In [27]: a.ctypes.get_as_parameter() Out[27]: c_void_p(27442576) You might want to use the new ctypes-based OpenGL 3.0+ package. It has numpy support a bit more directly. You can use Pyglet for its windowing and all of the other surrounding infrastructure and use OpenGL directly for the drawing. -- Robert Kern I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth. -- Umberto Eco ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image
Thanks for the suggestions, everyone! All very informative and most helpful. For what it's worth, here's my application: I'm building a tool for image processing which needs some manual input in a few places (e.g. user draws a few lines). The images are greyscale images with 12-14 bits of dynamic range (from a microscope), so I need to have some basic brightness/contrast/gamma controls, as well as allowing basic drawing on the image to get the needed user input. It looks like GL or wx will be best suited here, I think? (I presume that python/numpy/ [GL|wx] can keep up with things like dragging a slider to change brightness/contrast/other LUT changes, as long as I code reasonably.) Anyhow, thanks for all the input, Zach On Nov 29, 2007, at 9:03 PM, Joe Harrington wrote: If you want to explore the array interactively, blink images, mess with colormaps using the mouse, rescale the image values, mark regions, add labels, look at dynamic plots of rows and columns, etc., get the ds9 image viewer and the xpa programs that come with it that allow it to communicate with other programs: ftp://sao-ftp.harvard.edu/pub/rd/ds9 http://hea-www.harvard.edu/RD/ds9/index.html Then get the Python numdisplay package, which uses xpa. You have to get numdisplay from inside the stsci_python package: http://www.stsci.edu/resources/software_hardware/pyraf/stsci_python/ current/download Just grab the numdisplay directory from within that. Older versions of numdisplay are standalone but don't work perfectly. Beware, there are outdated web sites about numdisplay on the stsci site. Don't google! Run ds9 before you load numdisplay. Then you can send your python arrays to a real interactive data viewer at will. There are even mechanisms to define physical coordinates mapped from the image coordinates. --jh-- ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] display numpy array as image
If you want to explore the array interactively, blink images, mess with colormaps using the mouse, rescale the image values, mark regions, add labels, look at dynamic plots of rows and columns, etc., get the ds9 image viewer and the xpa programs that come with it that allow it to communicate with other programs: ftp://sao-ftp.harvard.edu/pub/rd/ds9 http://hea-www.harvard.edu/RD/ds9/index.html Then get the Python numdisplay package, which uses xpa. You have to get numdisplay from inside the stsci_python package: http://www.stsci.edu/resources/software_hardware/pyraf/stsci_python/current/download Just grab the numdisplay directory from within that. Older versions of numdisplay are standalone but don't work perfectly. Beware, there are outdated web sites about numdisplay on the stsci site. Don't google! Run ds9 before you load numdisplay. Then you can send your python arrays to a real interactive data viewer at will. There are even mechanisms to define physical coordinates mapped from the image coordinates. --jh-- ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
