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I use sympy plotting backends library to create plots directly from sympy expressions. As backends i use matplotlib library. Actually, i don't need to show a plot. I create plot and then i return it as svg string in order to insert it in a web page later. Everything worked fine, but when i started to use new virtual environment (i installed all necessary packages) i got an error. I use the following code:
# create two plot: one from init_expr (sympy tree expression) and second from
# fourier_expr (sympy tree expression):
p1 = plot(
(init_expr, (var, left_bound, right_bound), label_1, line_color_1),
(fourier_expr, (var, left_bound, right_bound), label_2, line_color_2),
show = False)
# add axes decorations and legend:
p1.xlabel = var_name
p1.ylabel = "f(" + data.var_name + ")"
p1.legend = True
# buffer to write svg data:
f = io.StringIO()
# save plot in svg formate in buffer:
p1.save(f, format = "svg")
# return svg string:
return f.getvalue()
when execution begins, at line:
p1.save(f, format="svg")
i get an error:
AttributeError("'NoneType' object has no attribute 'runner'")
Any ideas what am i doing wrong?
I have a pan-tilt-zoom camera (changing focal length over time). There is no idea about its base focal length (e.g. focal length in time point 0). However, It is possible to track the change in focal length between frame and another based on some known constraints and assumptions (Doing a SLAM).
If I assume a random focal length (in pixel unit), for example, 1000 pixel. Then, the new focal lengths are tracked frame by frame. Would I get correct results relatively? Would the results (focal lengths) in each frame be correct up to scale to the ground truth focal length?
For pan and tilt, assuming 0 at start would be valid. Although it is not correct, The estimated values of new tili-pan will be correct up to an offset. However, I suspect the estimated focal length will not be even correct up to scale or offset.. Is it correct or not?
For a quick short answer - if pan-tilt-zoom camera is approximated as a thin lens, then this is the relation between distance (z) and focal length (f):
This is just an approximation. Not fully correct. For more precise calculations, see the camera matrix. Focal length is an intrinsic parameter in the camera matrix. Even if not known, it can be calculated using some camera calibration method such as DLT, Zhang's Method and RANSAC. Once you have the camera matrix, focal length is just a small part of it. You get many more useful things along with it.
OpenCV has an inbuilt implementation of Zhang's method. (Look at this documentation for explanations, but code is old and unusable. New up-to-date code below.) You need to take some pictures of a chess board through your camera. Here is some helper code:
import cv2
from matplotlib import pyplot as plt
import numpy as np
from glob import glob
from scipy import linalg
x,y = np.meshgrid(range(6),range(8))
world_points=np.hstack((x.reshape(48,1),y.reshape(48,1),np.zeros((48,1)))).astype(np.float32)
_3d_points=[]
_2d_points=[]
img_paths=glob('./*.JPG') #get paths of all checkerboard images
for path in img_paths:
im=cv2.imread(path)
ret, corners = cv2.findChessboardCorners(im, (6,8))
if ret: #add points only if checkerboard was correctly detected:
_2d_points.append(corners) #append current 2D points
_3d_points.append(world_points) #3D points are always the same
ret, mtx, dist, rvecs, tvecs = cv2.calibrateCamera(_3d_points, _2d_points, (im.shape[1],im.shape[0]), None, None)
print ("Ret:\n",ret)
print ("Mtx:\n",mtx)
print ("Dist:\n",dist)
You might want Undistortion: Correcting for Radial Distortion
# termination criteria
criteria = (cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 30, 0.001)
# prepare object points, like (0,0,0), (1,0,0), (2,0,0) ....,(6,5,0)
objp = np.zeros((6*8,3), np.float32)
objp[:,:2] = np.mgrid[0:6,0:8].T.reshape(-1,2)
# Arrays to store object points and image points from all the images.
objpoints = [] # 3d point in real world space
imgpoints = [] # 2d points in image plane.
for fname in img_paths:
img = cv2.imread(fname)
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# Find the chess board corners
ret, corners = cv2.findChessboardCorners(gray, (6,8),None)
# If found, add object points, image points (after refining them)
if ret == True:
objpoints.append(objp)
cv2.cornerSubPix(gray,corners,(11,11),(-1,-1),criteria)
imgpoints.append(corners)
if 'IMG_5456.JPG' in fname:
plt.figure(figsize=(20,10))
img_vis=img.copy()
cv2.drawChessboardCorners(img_vis, (6,8), corners, ret)
plt.imshow(img_vis)
plt.show()
#Calibration
ret, mtx, dist, rvecs, tvecs = cv2.calibrateCamera(objpoints, imgpoints, gray.shape[::-1],None,None)
# Reprojection Error
tot_error = 0
for i in range(len(objpoints)):
imgpoints2, _ = cv2.projectPoints(objpoints[i], rvecs[i], tvecs[i], mtx, dist)
error = cv2.norm(imgpoints[i],imgpoints2, cv2.NORM_L2)/len(imgpoints2)
tot_error += error
print ("Mean Reprojection error: ", tot_error/len(objpoints))
# undistort
mapx,mapy = cv2.initUndistortRectifyMap(mtx,dist,None,newcameramtx,(w,h),5)
dst = cv2.remap(img,mapx,mapy,cv2.INTER_LINEAR)
# crop the image
x,y,w,h = roi
dst = dst[y:y+h, x:x+w]
plt.figure(figsize=(20,10))
#cv2.drawChessboardCorners(dst, (6,8), corners, ret)
plt.imshow(dst)
plt.show()
# Reprojection Error
tot_error = 0
for i in range(len(objpoints)):
imgpoints2, _ = cv2.projectPoints(objpoints[i], rvecs[i], tvecs[i], mtx, dist)
error = cv2.norm(imgpoints[i],imgpoints2, cv2.NORM_L2)/len(imgpoints2)
tot_error += error
print ("Mean Reprojection error: ", tot_error/len(objpoints))
I'm working on line plotting a metric for a course module as well as each of its questions within a Jupyter Notebook using %matplotlib notebook. That part is no problem. A module has typically 20-35 questions, so it results in a lot of lines on a chart. Therefore, I am plotting the metric for each question in a low alpha and I want to change the alpha and display the question name when I hover over the line, then reverse those when no longer hovering over the line.
The thing is, I've tried every test version of interactivity from the matplotlib documentation on event handling, as well as those in this question. It seems like the mpl_connect event is never firing, whether I use click or hover.
Here's a test version with a reduced dataset using the solution to the question linked above. Am I missing something necessary to get events to fire?
def update_annot(ind):
x,y = line.get_data()
annot.xy = (x[ind["ind"][0]], y[ind["ind"][0]])
text = "{}, {}".format(" ".join(list(map(str,ind["ind"]))),
" ".join([names[n] for n in ind["ind"]]))
annot.set_text(text)
annot.get_bbox_patch().set_alpha(0.4)
def hover(event):
vis = annot.get_visible()
if event.inaxes == ax:
cont, ind = line.contains(event)
if cont:
update_annot(ind)
annot.set_visible(True)
fig.canvas.draw_idle()
else:
if vis:
annot.set_visible(False)
fig.canvas.draw_idle()
module = 'bd2bc472-ee0d-466f-8557-788cc6de3018'
module_metrics[module] = {
'q_count': 31,
'sequence_pks': [0.5274546300604932,0.5262044653349001,0.5360993905297703,0.5292329279700655,0.5268691588785047,0.5319099014547161,0.5305164319248826,0.5268235294117647,0.573648805381582,0.5647933116581514,0.5669839795681448,0.5646591970121382,0.5663157894736842,0.5646976090014064,0.5659005628517824,0.5693634879925391,0.5728268468888371,0.5668834184858337,0.5687237026647967,0.5795640965549567,0.5877684407096172,0.585690904839841,0.5766899766899767,0.5971341320178529,0.6059972105997211,0.6055516678329834,0.6209865053513262,0.6203121360354065,0.6153666510976179,0.6236909471724459,0.6387654898293196],
'q_pks': {
'0da04f02-4aad-4ac8-91a5-214862b5c0d0': [0.6686046511627907,0.6282051282051282,0.76,0.6746987951807228,0.7092198581560284,0.71875,0.6585365853658537,0.7070063694267515,0.7171052631578947,0.7346938775510204,0.7737226277372263,0.7380952380952381,0.6774193548387096,0.7142857142857143,0.7,0.6962962962962963,0.723404255319149,0.6737588652482269,0.7232704402515723,0.7142857142857143,0.7164179104477612,0.7317073170731707,0.6333333333333333,0.75,0.7217391304347827,0.7017543859649122,0.7333333333333333,0.7641509433962265,0.6869565217391305,0.75,0.794392523364486],
'10bd29aa-3a26-49e6-bc2c-50fd503d7ab5': [0.64375,0.6014492753623188,0.5968992248062015,0.5059523809523809,0.5637583892617449,0.5389221556886228,0.5576923076923077,0.51875,0.4931506849315068,0.5579710144927537,0.577922077922078,0.5467625899280576,0.5362318840579711,0.6095890410958904,0.5793103448275863,0.5159235668789809,0.6196319018404908,0.6143790849673203,0.5035971223021583,0.5897435897435898,0.5857142857142857,0.5851851851851851,0.6164383561643836,0.6054421768707483,0.5714285714285714,0.627906976744186,0.5826771653543307,0.6504065040650406,0.5864661654135338,0.6333333333333333,0.6851851851851852]
}}
suptitle_size = 24
title_size = 18
tick_size = 12
axis_label_size = 15
legend_size = 14
fig, ax = plt.subplots(figsize=(15,8))
fig.suptitle('PK by Sequence Order', fontsize=suptitle_size)
module_name = 'Test'
q_count = module_metrics[module]['q_count']
y_ticks = [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0]
x_ticks = np.array([x for x in range(0,q_count)])
x_labels = x_ticks + 1
# Plot it
ax.set_title(module_name, fontsize=title_size)
ax.set_xticks(x_ticks)
ax.set_yticks(y_ticks)
ax.set_xticklabels(x_labels, fontsize=tick_size)
ax.set_yticklabels(y_ticks, fontsize=tick_size)
ax.set_xlabel('Sequence', fontsize=axis_label_size)
ax.set_xlim(-0.5,q_count-0.5)
ax.set_ylim(0,1)
ax.grid(which='major',axis='y')
# Output module PK by sequence
ax.plot(module_metrics[module]['sequence_pks'])
# Output PK by sequence for each question
for qid in module_metrics[module]['q_pks']:
ax.plot(module_metrics[module]['q_pks'][qid], alpha=0.15, label=qid)
annot = ax.annotate("", xy=(0,0), xytext=(-20,20),textcoords="offset points", bbox=dict(boxstyle="round", fc="w"), arrowprops=dict(arrowstyle="->"))
annot.set_visible(False)
mpl_id = fig.canvas.mpl_connect('motion_notify_event', hover)
Since there are dozens of modules, I created an ipywidgets dropdown to select the module, which then runs a function to output the chart. Nonetheless, whether running it hardcoded as here or from within the function, mpl_connect never seems to fire.
Here's what this one looks like when run
I applied facebook network sample from this documentation on my work, to get this code:
edges_df = pd.read_csv('rel.csv', delimiter= ";")
nodes_df = pd.read_csv('monfichier.csv', delimiter= ";")
padding = dict(x=(-1.1, 1.1), y=(-1.1, 1.1))
fb_nodes = hv.Dataset(nodes_df, 'index')
fb_graph = hv.Graph((edges_df, fb_nodes)).redim.range(**padding)
colors = ['#000000'] + hv.Cycle('Category20').values
fb_graph.opts(color_index='age', show_frame=False,
xaxis=True, yaxis=True, node_size=10, edge_line_width=1, cmap=colors)
renderer = hv.renderer('bokeh')
plot = renderer.get_plot(fb_graph).state
show(plot)
It works fine. But the resulted network was a graph without a specific layout (as shown in attached figure). I want to specify the network layout as in networkx. How to do that ?
I found, this instruction:
hv.Graph.from_networkx(G, nx.layout.spring_layout).opts(tools=['hover'])
But I did not find how to use it with my code, since my G is already an holoview and not a networkx graph.
Do you have any suggestion ?
There is a function called layout_nodes in HoloViews which can apply networkx (and other) layouts to an existing graph:
N = 8
node_indices = np.arange(N)
source = np.zeros(N)
target = node_indices
padding = dict(x=(-1.2, 1.2), y=(-1.2, 1.2))
simple_graph = hv.Graph(((source, target),)).redim.range(**padding)
hv.element.graphs.layout_nodes(simple_graph, layout=nx.spring_layout)
For those that want to export a simple 3D numpy array (along with axes) to a .vtk (or .vtr) file for post-processing and display in Paraview or Mayavi there's a little module called PyEVTK that does exactly that. The module supports structured and unstructured data etc..
Unfortunately, even though the code works fine in unix-based systems I couldn't make it work (keeps crashing) on any windows installation which simply makes things complicated. Ive contacted the developer but his suggestions did not work
Therefore my question is:
How can one use the from vtk.util import numpy_support function to export a 3D array (the function itself doesn't support 3D arrays) to a .vtk file? Is there a simple way to do it without creating vtkDatasets etc etc?
Thanks a lot!
It's been forever and I had entirely forgotten asking this question but I ended up figuring it out. I've written a post about it in my blog (PyScience) providing a tutorial on how to convert between NumPy and VTK. Do take a look if interested:
pyscience.wordpress.com/2014/09/06/numpy-to-vtk-converting-your-numpy-arrays-to-vtk-arrays-and-files/
It's not a direct answer to your question, but if you have tvtk (if you have mayavi, you should have it), you can use it to write your data to vtk format. (See: http://code.enthought.com/projects/files/ETS3_API/enthought.tvtk.misc.html )
It doesn't use PyEVTK, and it supports a broad range of data sources (more than just structured and unstructured grids), so it will probably work where other things aren't.
As a quick example (Mayavi's mlab interface can make this much less verbose, especially if you're already using it.):
import numpy as np
from enthought.tvtk.api import tvtk, write_data
data = np.random.random((10,10,10))
grid = tvtk.ImageData(spacing=(10, 5, -10), origin=(100, 350, 200),
dimensions=data.shape)
grid.point_data.scalars = np.ravel(order='F')
grid.point_data.scalars.name = 'Test Data'
# Writes legacy ".vtk" format if filename ends with "vtk", otherwise
# this will write data using the newer xml-based format.
write_data(grid, 'test.vtk')
And a portion of the output file:
# vtk DataFile Version 3.0
vtk output
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 10 10 10
SPACING 10 5 -10
ORIGIN 100 350 200
POINT_DATA 1000
SCALARS Test%20Data double
LOOKUP_TABLE default
0.598189 0.228948 0.346975 0.948916 0.0109774 0.30281 0.643976 0.17398 0.374673
0.295613 0.664072 0.307974 0.802966 0.836823 0.827732 0.895217 0.104437 0.292796
0.604939 0.96141 0.0837524 0.498616 0.608173 0.446545 0.364019 0.222914 0.514992
...
...
TVTK of Mayavi has a beautiful way of writing vtk files. Here is a test example I have written for myself following #Joe and tvtk documentation. The advantage it has over evtk, is the support for both ascii and html.Hope it will help other people.
from tvtk.api import tvtk, write_data
import numpy as np
#data = np.random.random((3, 3, 3))
#
#i = tvtk.ImageData(spacing=(1, 1, 1), origin=(0, 0, 0))
#i.point_data.scalars = data.ravel()
#i.point_data.scalars.name = 'scalars'
#i.dimensions = data.shape
#
#w = tvtk.XMLImageDataWriter(input=i, file_name='spoints3d.vti')
#w.write()
points = np.array([[0,0,0], [1,0,0], [1,1,0], [0,1,0]], 'f')
(n1, n2) = points.shape
poly_edge = np.array([[0,1,2,3]])
print n1, n2
## Scalar Data
#temperature = np.array([10., 20., 30., 40.])
#pressure = np.random.rand(n1)
#
## Vector Data
#velocity = np.random.rand(n1,n2)
#force = np.random.rand(n1,n2)
#
##Tensor Data with
comp = 5
stress = np.random.rand(n1,comp)
#
#print stress.shape
## The TVTK dataset.
mesh = tvtk.PolyData(points=points, polys=poly_edge)
#
## Data 0 # scalar data
#mesh.point_data.scalars = temperature
#mesh.point_data.scalars.name = 'Temperature'
#
## Data 1 # additional scalar data
#mesh.point_data.add_array(pressure)
#mesh.point_data.get_array(1).name = 'Pressure'
#mesh.update()
#
## Data 2 # Vector data
#mesh.point_data.vectors = velocity
#mesh.point_data.vectors.name = 'Velocity'
#mesh.update()
#
## Data 3 additional vector data
#mesh.point_data.add_array( force)
#mesh.point_data.get_array(3).name = 'Force'
#mesh.update()
mesh.point_data.tensors = stress
mesh.point_data.tensors.name = 'Stress'
# Data 4 additional tensor Data
#mesh.point_data.add_array(stress)
#mesh.point_data.get_array(4).name = 'Stress'
#mesh.update()
write_data(mesh, 'polydata.vtk')
# XML format
# Method 1
#write_data(mesh, 'polydata')
# Method 2
#w = tvtk.XMLPolyDataWriter(input=mesh, file_name='polydata.vtk')
#w.write()
I know it is a bit late and I do love your tutorials #somada141. This should work too.
def numpy2VTK(img, spacing=[1.0, 1.0, 1.0]):
# evolved from code from Stou S.,
# on http://www.siafoo.net/snippet/314
# This function, as the name suggests, converts numpy array to VTK
importer = vtk.vtkImageImport()
img_data = img.astype('uint8')
img_string = img_data.tostring() # type short
dim = img.shape
importer.CopyImportVoidPointer(img_string, len(img_string))
importer.SetDataScalarType(VTK_UNSIGNED_CHAR)
importer.SetNumberOfScalarComponents(1)
extent = importer.GetDataExtent()
importer.SetDataExtent(extent[0], extent[0] + dim[2] - 1,
extent[2], extent[2] + dim[1] - 1,
extent[4], extent[4] + dim[0] - 1)
importer.SetWholeExtent(extent[0], extent[0] + dim[2] - 1,
extent[2], extent[2] + dim[1] - 1,
extent[4], extent[4] + dim[0] - 1)
importer.SetDataSpacing(spacing[0], spacing[1], spacing[2])
importer.SetDataOrigin(0, 0, 0)
return importer
Hope it helps!
Here's a SimpleITK version with the function load_itk taken from here:
import SimpleITK as sitk
import numpy as np
if len(sys.argv)<3:
print('Wrong number of arguments.', file=sys.stderr)
print('Usage: ' + __file__ + ' input_sitk_file' + ' output_sitk_file', file=sys.stderr)
sys.exit(1)
def quick_read(filename):
# Read image information without reading the bulk data.
file_reader = sitk.ImageFileReader()
file_reader.SetFileName(filename)
file_reader.ReadImageInformation()
print('image size: {0}\nimage spacing: {1}'.format(file_reader.GetSize(), file_reader.GetSpacing()))
# Some files have a rich meta-data dictionary (e.g. DICOM)
for key in file_reader.GetMetaDataKeys():
print(key + ': ' + file_reader.GetMetaData(key))
def load_itk(filename):
# Reads the image using SimpleITK
itkimage = sitk.ReadImage(filename)
# Convert the image to a numpy array first and then shuffle the dimensions to get axis in the order z,y,x
data = sitk.GetArrayFromImage(itkimage)
# Read the origin of the ct_scan, will be used to convert the coordinates from world to voxel and vice versa.
origin = np.array(list(reversed(itkimage.GetOrigin())))
# Read the spacing along each dimension
spacing = np.array(list(reversed(itkimage.GetSpacing())))
return data, origin, spacing
def convert(data, output_filename):
image = sitk.GetImageFromArray(data)
writer = sitk.ImageFileWriter()
writer.SetFileName(output_filename)
writer.Execute(image)
def wait():
print('Press Enter to load & convert or exit using Ctrl+C')
input()
quick_read(sys.argv[1])
print('-'*20)
wait()
data, origin, spacing = load_itk(sys.argv[1])
convert(sys.argv[2])