python vtk XMLPolyDataWriter write solid tetrahedrons - python

I need to write a xml vtk file in python with solids tetrahedrons. Specifically in a Polydata. I have a collection of tetrahedrons with x,y,z coordinates of each edge. I try to use vtk.vtkXMLPolyDataWriter() but I get this (only 2D triangles):
enter image description here
My code :
#!/usr/bin/env python
import vtk
points = vtk.vtkPoints()
points.InsertNextPoint(0, 0, 0)
points.InsertNextPoint(1, 0, 0)
points.InsertNextPoint(1, 1, 0)
points.InsertNextPoint(0, 1, 1)
tetra = vtk.vtkTetra()
tetra.GetPointIds().SetId(0, 0)
tetra.GetPointIds().SetId(1, 1)
tetra.GetPointIds().SetId(2, 2)
tetra.GetPointIds().SetId(3, 3)
cellArray = vtk.vtkCellArray()
cellArray.InsertNextCell(tetra)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetPolys(cellArray)
polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5:
polydata.Update()
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName("Primal_geo.vtp");
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(polydata)
else:
writer.SetInputData(polydata)
writer.Write()
So, how can i write this file?
Thanks!

XML is information in tags. It is kind of a free hand json.
So here we go.
Now let me start by saying that I am not familiar with vtk or it's features, so while I hope the code I provide here serves your purposes I am not sure that a more satisfactory (preexisting piece of vtk) doesn't exist.
That said I wrote this little something up.
#!/usr/bin/env python
import vtk
class vtkXMLparser:
points = None
scellArray = None
def tagSplit(self,line):
for n,k in enumerate(line):
go = none
fin = none
if(k == ">"):
if(go == none):
if(n>0):
if(line[n-1]!="\\"):
go = n+1
if(go != none):
if(k == "<"):
if(n>0):
if(line[n-1]!="\\"):
if(n<len(line)-1):
if(line[n+1]=="/"):
fin = n+1
tag = line[fin+2:len(line)-1]
content = line[go:fin]
return([tag,content])
def addNice(self,di,key,cont):
try:
di[key].append(cont)
except(KeyError):
di[key]=[]
di[key].append(cont)
def parse(self,f):
input = open(f,"r")
xml = input.read()
xml = xml.split("\n")
data = {}
for lineNumber,line in enumerate(xml):
parsedXmlLine = self.tagSplit(line)
self.addNice(data,parsedXmlLine[0],parsedXmlLine[1])
self.self.points(data)
self.tetra(data)
self.write()
def self.points(self,di):
self.points = vtk.vtkself.points()
for point in di["point"]:
self.points.InsertNextPoint(eval(point))
def tetra(self,di):
tetra = vtk.vtkTetra()
for id in di["tetra"]:
tetra.GetPointIds().SetId(eval(id))
self.cellArray = vtk.vtkself.cellArray()
self.cellArray.InsertNextCell(tetra)
def write(self):
polydata = vtk.vtkPolyData()
polydata.Setself.points(self.points)
polydata.SetPolys(self.cellArray)
polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5:
polydata.Update()
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName("Primal_geo.vtp");
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(polydata)
else:
writer.SetInputData(polydata)
writer.Write()
i = vtkXMLparser()
i.parse("input.xml")
I would write an input file that looks something like this for your example.
<point>0, 0, 0</point>
<point>1, 0, 0</point>
<point>1, 1, 0</point>
<point>0, 1, 1</point>
<tetra>0, 0</tetra>
<tetra>1, 1</tetra>
<tetra>2, 2</tetra>
<tetra>3, 3</tetra>
I hope this helps!

Related

Python Chess Data (FEN) into Stockfish for Python

I am trying to use stockfish to evaluate a chess position using FEN notation all in Python. I am mainly using two libraries (pgnToFen I found on github here: https://github.com/SindreSvendby/pgnToFen and Stockfish the MIT licensed one here: https://github.com/zhelyabuzhsky/stockfish). After many bugs I have reached problem after problem. Stockfish not only can't analyse this FEN position (3b2k1/1p3pp1/8/3pP1P1/pP3P2/P2pB3/6K1/8 b f3 -) but it infinitely loops! "No worries!" and thought changing the source code would be accomplishable. Changed to _put(), but basically I am unable to put dummy values in because stdin.flush() won't execute once I give it those values! Meaning I don't even think I can skip to the next row in my dataframe. :( The code I changed is below.
def _put(self, command: str, tmp_time) -> None:
if not self.stockfish.stdin:
raise BrokenPipeError()
self.stockfish.stdin.write(f"{command}\n")
try:
self.stockfish.stdin.flush()
except:
if command != "quit":
self.stockfish.stdin.write('isready\n')
try:
time.sleep(tmp_time)
self.stockfish.stdin.flush()
except:
#print ('Imma head out', file=sys.stderr)
raise ValueError('Imma head out...')
#sys.stderr.close()
def get_evaluation(self) -> dict:
"""Evaluates current position
Returns:
A dictionary of the current advantage with "type" as "cp" (centipawns) or "mate" (checkmate in)
"""
evaluation = dict()
fen_position = self.get_fen_position()
if "w" in fen_position: # w can only be in FEN if it is whites move
compare = 1
else: # stockfish shows advantage relative to current player, convention is to do white positive
compare = -1
self._put(f"position {fen_position}", 5)
self._go()
x=0
while True:
x=x+1
text = self._read_line()
#print(text)
splitted_text = text.split(" ")
if splitted_text[0] == "info":
for n in range(len(splitted_text)):
if splitted_text[n] == "score":
evaluation = {
"type": splitted_text[n + 1],
"value": int(splitted_text[n + 2]) * compare,
}
elif splitted_text[0] == "bestmove":
return evaluation
elif x == 500:
evaluation = {
"type": 'cp',
"value": 10000,
}
return evaluation
and last but not least change to the init_ contructor below:
self._stockfish_major_version: float = float(self._read_line().split(" ")[1])
And the code where I am importing this code to is below, this is where errors pop up.
import pandas as pd
import re
import nltk
import numpy as np
from stockfish import Stockfish
import os
import sys
sys.path.insert(0, r'C:\Users\path\to\pgntofen')
import pgntofen
#nltk.download('punkt')
#Changed models.py for major version line 39 in stockfish from int to float
stockfish = Stockfish(r"C:\Users\path\to\Stockfish.exe")
file = r'C:\Users\path\to\selenium-pandas output.csv'
chunksize = 10 ** 6
for chunk in pd.read_csv(file, chunksize=chunksize):
for index, row in chunk.iterrows():
FullMovesStr = str(row['FullMoves'])
FullMovesStr = FullMovesStr.replace('+', '')
if "e.p" in FullMovesStr:
row.to_csv(r'C:\Users\MyName\Logger.csv', header=None, index=False, mode='a')
print('Enpassant')
continue
tokens = nltk.word_tokenize(FullMovesStr)
movelist = []
for tokenit in range(len(tokens)):
if "." in str(tokens[tokenit]):
try:
tokenstripped = re.sub(r"[0-9]+\.", "", tokens[tokenit])
token = [tokenstripped, tokens[tokenit+1]]
movelist.append(token)
except:
continue
else:
continue
DFMoves = pd.DataFrame(movelist, columns=[['WhiteMove', 'BlackMove']])
DFMoves['index'] = row['index']
DFMoves['Date'] = row['Date']
DFMoves['White'] = row['White']
DFMoves['Black'] = row['Black']
DFMoves['W ELO'] = row['W ELO']
DFMoves['B ELO'] = row['B ELO']
DFMoves['Av ELO'] = row['Av ELO']
DFMoves['Event'] = row['Event']
DFMoves['Site'] = row['Site']
DFMoves['ECO'] = row['ECO']
DFMoves['Opening'] = row['Opening']
pd.set_option('display.max_rows', DFMoves.shape[0]+1)
print(DFMoves[['WhiteMove', 'BlackMove']])
seqmoves = []
#seqmovesBlack = []
evalmove = []
pgnConverter = pgntofen.PgnToFen()
#stockfish.set_fen_position("rnbqkbnr/pppppppp/8/8/8/8/PPPPPPPP/RNBQKBNR w KQkq - 0 1")
#rnbqkbnr/pppppppp/8/8/8/8/PPPPPPPP/RNBQKBNR w KQkq - 0 1
for index, row in DFMoves.iterrows():
try:
stockfish.set_fen_position("rnbqkbnr/pppppppp/8/8/8/8/PPPPPPPP/RNBQKBNR w KQkq - 0 1")
except:
evalmove.append("?")
continue
#stockfish.set_fen_position("rnbqkbnr/pppppppp/8/8/8/8/PPPPPPPP/RNBQKBNR w KQkq - 0 1")
pgnConverter.resetBoard()
WhiteMove = str(row['WhiteMove'])
BlackMove = str(row['BlackMove'])
if index == 0:
PGNMoves1 = [WhiteMove]
seqmoves.append(WhiteMove)
#seqmoves.append(BlackMove)
else:
seqmoves.append(WhiteMove)
#seqmoves.append(BlackMove)
PGNMoves1 = seqmoves.copy()
#print(seqmoves)
try:
pgnConverter.pgnToFen(PGNMoves1)
fen = pgnConverter.getFullFen()
except:
break
try:
stockfish.set_fen_position(fen)
print(stockfish.get_board_visual())
evalpos = stockfish.get_evaluation()
evalmove.append(evalpos)
except:
pass
try:
stockfish.set_fen_position("rnbqkbnr/pppppppp/8/8/8/8/PPPPPPPP/RNBQKBNR w KQkq - 0 1")
except:
evalmove.append("?")
continue
pgnConverter.resetBoard()
if index == 0:
PGNMoves2 = [WhiteMove, BlackMove]
seqmoves.append(BlackMove)
else:
seqmoves.append(BlackMove)
PGNMoves2 = seqmoves.copy()
try:
pgnConverter.pgnToFen(PGNMoves2)
fen = pgnConverter.getFullFen()
except:
break
try:
stockfish.set_fen_position(fen)
print(stockfish.get_board_visual())
evalpos = stockfish.get_evaluation()
print(evalpos)
evalmove.append(evalpos)
except:
pass
#DFMoves['EvalWhite'] = evalwhite
#DFMoves['EvalBlack'] = evalblack
print(evalmove)
So the detailed question is getting stockfish.get_evalution() to just skip, or better yet fix the problem, for this ( 3b2k1/1p3pp1/8/3pP1P1/pP3P2/P2pB3/6K1/8 b f3 - ) FEN position. I have been working on this problem for quite a while so any insight into this would be very much appreciated.
My specs are Windows 10, Python 3.9, Processor:Intel(R) Core(TM) i9-10980XE CPU # 3.00GHz 3.00 GHz and RAM is 64.0 GB.
Thanks :)
Ok. It seems your fen is invalid (3b2k1/1p3pp1/8/3pP1P1/pP3P2/P2pB3/6K1/8 b f3 -). So check that. And python-chess (https://python-chess.readthedocs.io/en/latest/index.html) library allows you to use FEN AND chess engines. So, pretty cool no ? Here is an example of theses two fantastics tools :
import chess
import chess.engine
import chess.pgn
pgn = open("your_pgn_file.pgn")
game = chess.pgn.read_game(pgn)
engine = chess.engine.SimpleEngine.popen_uci("your_stockfish_path.exe")
# Iterate through all moves, play them on a board and analyse them.
board = game.board()
for move in game.mainline_moves():
board.push(move)
print(engine.analyse(board, chess.engine.Limit(time=0.1))["score"])

ModuleNotFoundError: No module named 'gtk'

I've tried to follow several solutions on the internet also this one, but no luck. I'm in the process of implementing a object detection system. I am on Windows 10, and using PyCharm using python-3.8
I am getting errors for the packages, I've tried to add them through the package installer and through the terminal, no luck. Here's the error:
Traceback (most recent call last):
File "D:/CabaleGame/runner.py", line 2, in <module>
import processCards
File "D:\CabaleGame\processCards.py", line 1, in <module>
import gtk.gdk
ModuleNotFoundError: No module named 'gtk'
Process finished with exit code 1
I've downloaded the package from here and here, which one is correct?
My program file:
import gtk.gdk
import cv
import time
import os
import string
def takeScreenCapture(screenShotNum = ""):
time.sleep(1)
w = gtk.gdk.get_default_root_window()
sz = w.get_size()
#print "The size of the window is %d x %d" % sz
pb = gtk.gdk.Pixbuf(gtk.gdk.COLORSPACE_RGB,False,8,sz[0],sz[1])
pb = pb.get_from_drawable(w,w.get_colormap(),0,0,0,0,sz[0],sz[1])
# Convert gtk.PixelBuf to a NumPy array
array = pb.get_pixels_array()
# Convert NumPy array to CvMat
mat = cv.fromarray(array)
# Convert RGB to BGR
cv.CvtColor(mat, mat, cv.CV_RGB2BGR)
#cv.ShowImage("win",mat)
#cv.WaitKey(0)
return mat
def getMeaningFromCards(cards):
"""
This takes a dictionary of the form:
(x, y) : Card image
and returns a dictionary of the form:
(x, y) : (number, suit)
(x, y) are the coordinates of the top left of the card
"""
imgdir = "LibraryImages"
templatesNums = os.listdir(os.path.join(imgdir,"Numbers"))
templatesSuits = os.listdir(os.path.join(imgdir,"Suits"))
#templates = filter(lambda s: s[-4:] == ".png", templates)
templatesNums = map(lambda s: os.path.join(imgdir,"Numbers", s), templatesNums)
templatesSuits = map(lambda s: os.path.join(imgdir, "Suits", s), templatesSuits)
for k in cards.keys():
card = cards[k]
cardImg = cv.CreateImageHeader((card.width, card.height), 8, 3)
cv.SetData(cardImg, card.tostring())
numAndSuit3 = cv.GetSubRect(cardImg, (0,0,30,80))
numAndSuit1 = cv.CreateImage((numAndSuit3.width, numAndSuit3.height), 8, 1)
cv.CvtColor(numAndSuit3, numAndSuit1, cv.CV_RGB2GRAY)
# Convert the 1 channel grayscale to 3 channel grayscale
# (GRAY2RGB doesn't actually introduce color)
cv.CvtColor(numAndSuit1, numAndSuit3, cv.CV_GRAY2RGB)
num = findBestTemplateMatch(templatesNums, numAndSuit3)
suit = findBestTemplateMatch(templatesSuits, numAndSuit3)
#print num, suit
# If this image was recognized as a card, but didn't match
# any template, it shouldn't be in the list in the first place
if num == None or suit == None:
del cards[k]
continue
num = string.split(os.path.basename(num), '.')[0]
suit = string.split(os.path.basename(suit), '.')[0]
# The alternate file names have underscores
# after their names
if num[-1] == '_':
num = num[:-1]
if suit[-1] == '_':
suit = suit[:-1]
cards[k] = (num, suit)
#cv.ShowImage("NumandSuit", numAndSuit)
#cv.WaitKey(0)
print
cards
return cards
def findBestTemplateMatch(tplList, img):
"""
Compares img against a list of templates.
tplList is a list of string filenames of template images
Returns a tuple (num, suit) if a template is suitably matched
or None if not
"""
minTpl = 200 # arbitrarily large number
tString = None
for t in tplList:
tpl = cv.LoadImage(t)
w = img.width - tpl.width + 1
h = img.height - tpl.height + 1
result = cv.CreateImage((w,h), 32, 1)
cv.MatchTemplate(img, tpl, result, cv.CV_TM_SQDIFF_NORMED)
(minVal, maxVal, minLoc, maxLoc) = cv.MinMaxLoc(result)
#print t
#print (minVal, maxVal, minLoc, maxLoc)
# 0.2 found by experiment (the non-card images end up being around
# 0.25 - 0.28, and all the card images were much around 0.08 and less
if minVal < minTpl and minVal < 0.2:
minTpl = minVal
tString = t
#print minTpl, tString
#cv.ShowImage("win", img)
#cv.ShowImage("win2", result)
#cv.WaitKey(0)
return tString
def extractCards(fileName = None):
"""
Given an image, this will extract the cards from it.
This takes a filename as an optional argument
This filename should be the name of an image file.
This returns a dictionary of the form:
(x, y) : Card image
It is likely that the output from this will go to the
getMeaningFromCards() function.
"""
if fileName == None:
mat = takeScreenCapture()
else:
mat = cv.LoadImage(fileName)
# First crop the image: but only crop out the bottom.
# It is useful to have all dimensions accurate to the screen
# because otherwise they will throw off the mouse moving and clicking.
# Cropping out the bottom does not change anything in terms of the mouse.
unnec_top_distance = 130
unnec_bottom_distance = 40
margin = 50
submat = cv.GetSubRect(mat, (0,0,mat.width, mat.height - unnec_bottom_distance))
subImg = cv.CreateImageHeader((submat.width, submat.height), 8, 3)
cv.SetData(subImg, submat.tostring())
gray = cv.CreateImage((submat.width, submat.height), 8, 1)
cv.CvtColor(submat, gray, cv.CV_RGB2GRAY)
thresh = 250
max_value = 255
cv.Threshold(gray, gray, thresh, max_value, cv.CV_THRESH_BINARY)
cv.Not(gray,gray)
#cv.ShowImage("sub", submat)
#cv.WaitKey(0)
storage = cv.CreateMemStorage (0)
cpy = cv.CloneImage(gray)
contours = cv.FindContours( cpy, storage, cv.CV_RETR_LIST, cv.CV_CHAIN_APPROX_SIMPLE, (0,0) );
#contours = cv.ApproxPoly(contours, cv.CreateMemStorage(), cv.CV_POLY_APPROX_DP, 3, 1)
bboxes = []
if contours:
while(contours):
area = cv.ContourArea(contours)
# It turns out that all the cards are about 44000 in area...
# It would definitely be nice to have a better way to do this:
# ie, find the size of the card programmatically and use it then
if(area > 44000 and area < submat.width*submat.height*2/3):
bb = cv.BoundingRect(contours)
bboxes.append(bb)
contours = contours.h_next()
#drawBoundingBoxes(bboxes, submat)
# cards is a dictionary of the form:
# (x, y) : card
cards = {}
for box in bboxes:
card = cv.GetSubRect(subImg, box)
#cv.ShowImage("card", card)
#cv.WaitKey(0)
cards[(box[0], box[1])] = card
return cards
def drawBoundingBoxes(bb, img):
for b in bb:
x = b[0]
y = b[1]
width = b[2]
height = b[3]
cv.Rectangle(img, (x,y), (x+width, y+height), (0,255,0,0))
cv.ShowI
mage("bb", img)
cv.WaitKey(0)
def drawSquares(listWithPoints,img):
for l in listWithPoints:
for p in range(len(l)-1):
cv.Line(img, l[p], l[p+1], (0,0,255,0),2)
cv.Line(img, l[-1], l[0], (0,0,255,0),2)
#cv.ShowImage("sub", img)
#cv.WaitKey(0)
def contourToPointList(contour):
plist = []
for (x,y) in contour:
plist.append((x,y))
return plist
if __name__ == '__main__':
cards = extractCards('CardImages/4_heart.jpg')
print
cards
#c = cards[cards.keys()[0]]
#print c
Is it possible to add it manually through the folders?
Would it work if i put the package her:
C:\Users\User1\AppData\Local\Programs\Python\Python38\include
From python documentation :
Replace import gtk.gdk by :
import gi
gi.require_version("Gtk", "insert your gtk version")
from gi.repository import Gtk

Setting row Span in QTableView using Python?

I am trying to set rowspan on second column of my QTableView but somehow logically i am missing something. i am only able to get A and B but not C. Plus i am getting warning QTableView::setSpan: span cannot overlap and QTableView::setSpan: single cell span won't be added
My code snippet is:-
startspan = 0
for i, tcname in enumerate(tcfilename):
if tcfilename[i]:
if i > 0:
print '#######################'
print 'startspan = '+str(startspan)+' i = '+str(i)
if tcname == tcfilename[i-1]:
#setSpan (row, column, rowSpan, columnSpan)
print 'if (from_row, till_row) '+str(startspan)+' '+str(i)
table_view.setSpan(startspan, 1, i, 1);
elif tcname != tcfilename[i-1]:
print 'Else no span (from_row, till_row) '+str(startspan)+' '+str(i)
table_view.setSpan(startspan, 1, i, 1);
if i == 1:
startspan = 0
else:
startspan = i
else:
break
Did this with simple two line code below
for toRow, tcname in enumerate(tcfilename):
table_view.setSpan(tcfilename.index(tcname), 1, tcfilename.count(tcname), 1)
I made a nifty little function to solve this.. Had recursion but then optimized it without recursion.. feed it a table and a data set
def my_span_checker(self, my_data, table):
for i in range(len(my_data)):
my_item_count = 0
my_label = table.item(i, 0).text()
for j in range(len(my_data)):
if table.item(j, 0).text() == my_label:
my_item_count += 1
if my_item_count != 1:
table.setSpan(i, 0, my_item_count, 1)

Parsing out data from files (Python): How to determine the number of republicans, democrats and independents in the 114th congress

So, I have been working on this bit of code to determine the number of senators from the 114th congress who were republicans, democrats, and independents. Here's my code. For some reason, I keep getting funky errors regarding my variables that start with num. Please help.
def main():
# Determines the number of senators of each party affiliation
infile = open("Senate114.txt", 'r')
set1 = {line.rstrip() + "\n" for line in infile}
infile.close()
listx = list(set1)
listx.sort(key=lambda x: x.split(',')[2]) # sort by party affiliation
partyAffiliation = listx[2]
rep = []
dem = []
ind = []
numRep = []
numDen = []
numInd = []
while (partyAffiliation == 'R'):
rep = rep.expend
numRep == int(len(rep))
while (partyAffiliation == 'D'):
dem = dem.extend
numDem == int(len(dem))
while (partyAffiliation == 'I',):
ind = ind.extend
numInd == int(len(ind))
print('Party Affiliation: ')
print('Republicans: ',numRep)
print('Democrats:' ,numDem)
print('Independents:' ,numInd)
main()
Assuming data that looks similar to this:
Gooding,Cuba,R
Miller,Dennis,D
Bolton,Michael,I
Grouch,Oscar,I
Einstein,Albert,R
Azaria,Hank,D
Motzart,Amadeus,I
You can use code like the following:
import collections
lines = open("Senate114.txt").read().splitlines()
parties = [line.split(",")[2] for line in lines]
party_counts = collections.Counter(parties)
print(party_counts)
OUTPUT
Counter({'I': 3, 'R': 2, 'D': 2})
You could add on:
print('Party Affiliations: ')
print('Republicans:', party_counts.get('R', 0))
print('Democrats:', party_counts.get('D', 0))
print('Independents:', party_counts.get('I', 0))

Data from a MATLAB .fig file using Python?

Does anyone know of any methods of extracting the data from a MATLAB fig file using Python? I know these are binary files but the methods in the Python Cookbook for .mat files http://www.scipy.org/Cookbook/Reading_mat_files don't seem to work for .fig files...
Thanks in advance for any help,
Dan
.fig files are .mat files (containing a struct), see
http://undocumentedmatlab.com/blog/fig-files-format/
As the reference you give states, structs are only supported up to v7.1:
http://www.scipy.org/Cookbook/Reading_mat_files
So, in MATLAB I save using -v7:
plot([1 2],[3 4])
hgsave(gcf,'c','-v7');
Then in Python 2.6.4 I use:
>>> from scipy.io import loadmat
>>> x = loadmat('c.fig')
>>> x
{'hgS_070000': array([[<scipy.io.matlab.mio5.mat_struct object at 0x1500e70>]], dtype=object), '__version__': '1.0', '__header__': 'MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Fri Nov 18 12:02:31 2011', '__globals__': []}
>>> x['hgS_070000'][0,0].__dict__
{'handle': array([[1]], dtype=uint8), 'children': array([[<scipy.io.matlab.mio5.mat_struct object at 0x1516030>]], dtype=object), '_fieldnames': ['type', 'handle', 'properties', 'children', 'special'], 'type': array([u'figure'], dtype='<U6'), 'properties': array([[<scipy.io.matlab.mio5.mat_struct object at 0x1500fb0>]], dtype=object), 'special': array([], shape=(1, 0), dtype=float64)}
Where I used .__dict__ to see how to traverse the structure. E.g. to get XData and YData I can use:
>>> x['hgS_070000'][0,0].children[0,0].children[0,0].properties[0,0].XData
array([[1, 2]], dtype=uint8)
>>> x['hgS_070000'][0,0].children[0,0].children[0,0].properties[0,0].YData
array([[3, 4]], dtype=uint8)
Showing that I'd used plot([1 2],[3 4]) in MATLAB (the child is the axis and the grandchild is the lineseries).
Here is my update from Sascha's post. Now it can:
display rotated, tex labels
display xticks and yticks
better handling of markers
grid on/off
better axes and legend enumeration handling
maintain figure size
The code is below:
from scipy.io import loadmat
import numpy as np
import matplotlib.pyplot as plt
def plotFig(filename,fignr=1):
d = loadmat(filename,squeeze_me=True, struct_as_record=False)
matfig = d['hgS_070000']
childs = matfig.children
ax1 = [c for c in childs if c.type == 'axes']
if(len(ax1) > 0):
ax1 = ax1[0]
legs = [c for c in childs if c.type == 'scribe.legend']
if(len(legs) > 0):
legs = legs[0]
else:
legs=0
pos = matfig.properties.Position
size = np.array([pos[2]-pos[0],pos[3]-pos[1]])/96
plt.figure(fignr,figsize=size)
plt.clf()
plt.hold(True)
counter = 0
for line in ax1.children:
if line.type == 'graph2d.lineseries':
if hasattr(line.properties,'Marker'):
mark = "%s" % line.properties.Marker
if(mark != "none"):
mark = mark[0]
else:
mark = '.'
if hasattr(line.properties,'LineStyle'):
linestyle = "%s" % line.properties.LineStyle
else:
linestyle = '-'
if hasattr(line.properties,'Color'):
r,g,b = line.properties.Color
else:
r = 0
g = 0
b = 1
if hasattr(line.properties,'MarkerSize'):
marker_size = line.properties.MarkerSize
else:
marker_size = -1
x = line.properties.XData
y = line.properties.YData
if(mark == "none"):
plt.plot(x,y,linestyle=linestyle,color=[r,g,b])
elif(marker_size==-1):
plt.plot(x,y,marker=mark,linestyle=linestyle,color=[r,g,b])
else:
plt.plot(x,y,marker=mark,linestyle=linestyle,color=[r,g,b],ms=marker_size)
elif line.type == 'text':
if counter == 0:
plt.xlabel("$%s$" % line.properties.String,fontsize =16)
elif counter == 1:
plt.ylabel("$%s$" % line.properties.String,fontsize = 16)
elif counter == 3:
plt.title("$%s$" % line.properties.String,fontsize = 16)
counter += 1
plt.grid(ax1.properties.XGrid)
if(hasattr(ax1.properties,'XTick')):
if(hasattr(ax1.properties,'XTickLabelRotation')):
plt.xticks(ax1.properties.XTick,ax1.properties.XTickLabel,rotation=ax1.properties.XTickLabelRotation)
else:
plt.xticks(ax1.properties.XTick,ax1.properties.XTickLabel)
if(hasattr(ax1.properties,'YTick')):
if(hasattr(ax1.properties,'YTickLabelRotation')):
plt.yticks(ax1.properties.YTick,ax1.properties.YTickLabel,rotation=ax1.properties.YTickLabelRotation)
else:
plt.yticks(ax1.properties.YTick,ax1.properties.YTickLabel)
plt.xlim(ax1.properties.XLim)
plt.ylim(ax1.properties.YLim)
if legs:
leg_entries = tuple(['$' + l + '$' for l in legs.properties.String])
py_locs = ['upper center','lower center','right','left','upper right','upper left','lower right','lower left','best','best']
MAT_locs=['North','South','East','West','NorthEast', 'NorthWest', 'SouthEast', 'SouthWest','Best','none']
Mat2py = dict(zip(MAT_locs,py_locs))
location = legs.properties.Location
plt.legend(leg_entries,loc=Mat2py[location])
plt.hold(False)
plt.show()
I found Alex's answer very appealing, but I extended his code a bit. First of all, I included the preamble to show where the figure, ylabel, etc. comes from. Second of all, I included the legend!
I'm rather new to Python, so any suggestions for improvements are highly welcomed.
def plotFig(filename,fignr=1):
from scipy.io import loadmat
from numpy import size
from matplotlib.pyplot import plot,figure,hold,xlabel,ylabel,show,clf,xlim,legend
d = loadmat(filename,squeeze_me=True, struct_as_record=False)
ax1 = d['hgS_070000'].children
if size(ax1) > 1:
legs= ax1[1]
ax1 = ax1[0]
else:
legs=0
figure(fignr)
clf()
hold(True)
counter = 0
for line in ax1.children:
if line.type == 'graph2d.lineseries':
if hasattr(line.properties,'Marker'):
mark = "%s" % line.properties.Marker
mark = mark[0]
else:
mark = '.'
if hasattr(line.properties,'LineStyle'):
linestyle = "%s" % line.properties.LineStyle
else:
linestyle = '-'
if hasattr(line.properties,'Color'):
r,g,b = line.properties.Color
else:
r = 0
g = 0
b = 1
if hasattr(line.properties,'MarkerSize'):
marker_size = line.properties.MarkerSize
else:
marker_size = 1
x = line.properties.XData
y = line.properties.YData
plot(x,y,marker=mark,linestyle=linestyle,color=color(r,g,b),markersize=marker_size)
elif line.type == 'text':
if counter < 1:
xlabel("%s" % line.properties.String,fontsize =16)
counter += 1
elif counter < 2:
ylabel("%s" % line.properties.String,fontsize = 16)
counter += 1
xlim(ax1.properties.XLim)
if legs:
leg_entries = tuple(legs.properties.String)
py_locs = ['upper center','lower center','right','left','upper right','upper left','lower right','lower left','best']
MAT_locs=['North','South','East','West','NorthEast', 'NorthWest', 'SouthEast', 'SouthWest','Best']
Mat2py = dict(zip(MAT_locs,py_locs))
location = legs.properties.Location
legend(leg_entries,loc=Mat2py[location])
hold(False)
show()
When you save a MATLAB figure, it dumps the Handle Graphics hierarchy into a structure, saves it to a .mat file, and changes the extension to .fig. So .fig files are just .mat files, and if the data you're looking for was stored somewhere in the original figure it will be in there. If you manually change the extension back to .mat you can load it into MATLAB and take a look.
I'm afraid I don't know much about reading .mat files from Python, but if you have a way of doing that in general, you should also be able to read in a .fig file.
This is much easier way available. It's based on the newer Scipy and loadmat:
http://answerpot.com/showthread.php?3707193-loadmat+and+figure
And my small extension to it for the simple 2D lines is:
from scipy.io import loadmat
d = loadmat('../impulse_all.fig',squeeze_me=True, struct_as_record=False)
# d = loadmat('R11_resuspension.fig',squeeze_me=True, struct_as_record=False)
ax1 = d['hgS_070000'].children
if size(ax1) > 1:
ax1 = ax1[0]
figure
hold(True)
counter = 0
for line in ax1.children:
if line.type == 'graph2d.lineseries':
marker = "%s" % line.properties.Marker
linestyle = "%s" % line.properties.LineStyle
r,g,b = line.properties.Color
marker_size = line.properties.MarkerSize
x = line.properties.XData
y = line.properties.YData
plot(x,y,marker,linestyle=linestyle,color = (r,g,b),markersize=marker_size)
elif line.type == 'text':
if counter < 1:
xlabel("%s" % line.properties.String,fontsize =16)
counter += 1
elif counter < 2:
ylabel("%s" % line.properties.String,fontsize = 16)
counter += 1
hold(False)
Using the posts of Sascha, I just wanted to extract the x-data and y-data stored in a .fig file.
Below is my python function, which is a simplification of the Sascha's function aiming at only extracting the data.
Output is a dictionary. Its keys are the corresponding labels of the data in the figure.
I put it there. Glad if this could save a few minutes to someone else !
import numpy
from scipy.io import loadmat
def read_fig(filename):
output = {}
d = loadmat(filename, squeeze_me=True, struct_as_record=False)
matfig = d['hgS_070000']
childs = matfig.children
ax1 = [c for c in childs if c.type == 'axes'][0]
for line in ax1.children:
try:
if line.type == 'graph2d.lineseries':
x = line.properties.XData
y = line.properties.YData
leg = line.properties.DisplayName
print leg
output[leg] = numpy.column_stack((x, y))
except:
print 'One children is ignored...'
return output

Categories