Does anybody know how to change or set the "Description" option/tag of a GeoTIFF file using GDAL?
To specify what I mean, this is an example of gdalinfo return from a GeoTIFF file with set "Description":
Band 1 Block=64x64 Type=UInt16, ColorInterp=Undefined
Description = AVHRR Channel 1: 0.58 micrometers -- 0.68 micrometers
Min=0.000 Max=814.000
Minimum=0.000, Maximum=814.000, Mean=113.177, StdDev=152.897
Metadata:
LAYER_TYPE=athematic
STATISTICS_MAXIMUM=814
STATISTICS_MEAN=113.17657236931
STATISTICS_MINIMUM=0
STATISTICS_STDDEV=152.89720574652
In the example you can see: Description = AVHRR Channel 1: 0.58 micrometers -- 0.68 micrometers
How do I set this parameter using GDAL?
In Python you can set the band description like this:
from osgeo import gdal, osr
import numpy
# Define output image name, size and projection info:
OutputImage = 'test.tif'
SizeX = 20
SizeY = 20
CellSize = 1
X_Min = 563220.0
Y_Max = 699110.0
N_Bands = 10
srs = osr.SpatialReference()
srs.ImportFromEPSG(2157)
srs = srs.ExportToWkt()
GeoTransform = (X_Min, CellSize, 0, Y_Max, 0, -CellSize)
# Create the output image:
Driver = gdal.GetDriverByName('GTiff')
Raster = Driver.Create(OutputImage, SizeX, SizeY, N_Bands, 2) # Datatype = 2 same as gdal.GDT_UInt16
Raster.SetProjection(srs)
Raster.SetGeoTransform(GeoTransform)
# Iterate over each band
for band in range(N_Bands):
BandNumber = band + 1
BandName = 'SomeBandName '+ str(BandNumber).zfill(3)
RasterBand = Raster.GetRasterBand(BandNumber)
RasterBand.SetNoDataValue(0)
RasterBand.SetDescription(BandName) # This sets the band name!
RasterBand.WriteArray(numpy.ones((SizeX, SizeY)))
# close the output image
Raster = None
print("Done.")
Unfortunately, I'm not sure if ArcGIS or QGIS are able to read the band descriptions. However, the band names are clearly visible in Tuiview:
GDAL includes a python application called gdal_edit.py which can be used to modify the metadata of a file in place. I am not familiar with the Description field you are referring to, but this tool should be the one to use.
Here is the man page: gdal_edit.py
Here is an example script using an ortho-image I downloaded from the USGS Earth-Explorer.
#!/bin/sh
# Image to modify
IMAGE_PATH='11skd505395.tif'
# Field to modify
IMAGE_FIELD='TIFFTAG_IMAGEDESCRIPTION'
# Print the tiff image description tag
gdalinfo $IMAGE_PATH | grep $IMAGE_FIELD
# Change the Field
CMD="gdal_edit.py -mo ${IMAGE_FIELD}='Lake-Tahoe' $IMAGE_PATH"
echo $CMD
$CMD
# Print the new field value
gdalinfo $IMAGE_PATH | grep $IMAGE_FIELD
Output
$ ./gdal-script.py
TIFFTAG_IMAGEDESCRIPTION=OrthoVista
gdal_edit.py -mo TIFFTAG_IMAGEDESCRIPTION='Lake-Tahoe' 11skd505395.tif
TIFFTAG_IMAGEDESCRIPTION='Lake-Tahoe'
Here is another link that should provide useful info.
https://gis.stackexchange.com/questions/111610/how-to-overwrite-metadata-in-a-tif-file-with-gdal
Here's a single purpose python commandline script to edit band description in place.
''' Set image band description to specified text'''
import os
import sys
from osgeo import gdal
gdal.UseExceptions()
if len(sys.argv) < 4:
print(f"Usage: {sys.argv[0]} [in_file] [band#] [text]")
sys.exit(1)
infile = sys.argv[1] # source filename and path
inband = int(sys.argv[2]) # source band number
descrip = sys.argv[3] # description text
data_in = gdal.Open(infile, gdal.GA_Update)
band_in = data_in.GetRasterBand(inband)
old_descrip = band_in.GetDescription()
band_in.SetDescription(descrip)
new_descrip = band_in.GetDescription()
# de-reference the datasets, which triggers gdal to save
data_in = None
data_out = None
print(f"Description was: {old_descrip}")
print(f"Description now: {new_descrip}")
In use:
$ python scripts\gdal-edit-band-desc.py test-edit.tif 1 "Red please"
Description was:
Description now: Red please
$ gdal-edit-band-desc test-edit.tif 1 "Red please also"
$ python t:\ENV.558\scripts\gdal-edit-band-desc.py test-edit.tif 1 "Red please also"
Description was: Red please
Description now: Red please also
Properly it should be added to gdal_edit.py but I don't know enough do feel safe adding it directly.
gdal_edit.py with the -mo flag can be used to edit the band descriptions, with the bands numbered starting from 1:
gdal_edit.py -mo BAND_1=AVHRR_Channel_1_p58_p68_um -mo BAND_2=AVHRR_Channel_2 avhrr.tif
I didn't try it with the special characters but that might work if you use the right quotes.
Related
I'm trying to learn how to split a pdf every n page.
In my case I want to split a 64p PDF into several chunks containing four pages each: file 1: p.1-4, file 2: p.5-8 etc.
I'm trying to understand PyPDF2 but my noobness overwhelms me:
from PyPDF2 import PdfFileWriter, PdfFileReader
pdf = PdfFileReader('my_pdf.pdf')
I guess I need to make a loop of sorts using addPage and write files till there's no pages left?
Little late but I ran into your question while looking for help trying to do the same thing.
I ended up doing the following, which does what you're asking. Mind you it's probably more than you're asking for, but the answer is in there. It's a rough first draft, in heavy need of refactoring and some variable renaming.
import os
from PyPDF2 import PdfFileReader, PdfFileWriter
def split_pdf(in_pdf, step=1):
"""Splits a given pdf into seperate pdfs and saves
those to a supfolder of the parent pdf's folder, called
splitted_pdf.
Arguments:
in_pdf: [str] Absolute path (and filename) of the
input pdf or just the filename, if the file
is in the current directory.
step: [int] Desired number of pages in each of the
output pdfs.
Returns:
dunno yet
"""
#TODO: Add choice for output dir
#TODO: Add logging instead of prints
#TODO: Refactor
try:
with open(in_pdf, 'rb') as in_file:
input_pdf = PdfFileReader(in_file)
num_pages = input_pdf.numPages
input_dir, filename = os.path.split(in_pdf)
filename = os.path.splitext(filename)[0]
output_dir = input_dir + "/" + filename + "_splitted/"
os.mkdir(output_dir)
intervals = range(0, num_pages, step)
intervals = dict(enumerate(intervals, 1))
naming = f'{filename}_p'
count = 0
for key, val in intervals.items():
output_pdf = PdfFileWriter()
if key == len(intervals):
for i in range(val, num_pages):
output_pdf.addPage(input_pdf.getPage(i))
nums = f'{val + 1}' if step == 1 else f'{val + 1}-{val + step}'
with open(f'{output_dir}{naming}{nums}.pdf', 'wb') as outfile:
output_pdf.write(outfile)
print(f'{naming}{nums}.pdf written to {output_dir}')
count += 1
else:
for i in range(val, intervals[key + 1]):
output_pdf.addPage(input_pdf.getPage(i))
nums = f'{val + 1}' if step == 1 else f'{val + 1}-{val + step}'
with open(f'{output_dir}{naming}{nums}.pdf', 'wb') as outfile:
output_pdf.write(outfile)
print(f'{naming}{nums}.pdf written to {output_dir}')
count += 1
except FileNotFoundError as err:
print('Cannot find the specified file. Check your input:')
print(f'{count} pdf files written to {output_dir}')
Hope it helps you.
from PyPDF2 import PdfFileReader, PdfFileWriter
import os
# Method to split the pdf at every given n pages.
def split_at_every(self,infile , step = 1):
# Copy the input file path to a local variable infile
input_pdf = PdfFileReader(open(infile, "rb"))
pdf_len = input_pdf.number_of_pages
# Get the complete file name along with its path and split the text to take only the first part.
fname = os.path.splitext(os.path.basename(infile))[0]
# Get the list of page numbers in the order of given step
# If there are 10 pages in a pdf, and the step is 2
# page_numbers = [0,2,4,6,8]
page_numbers = list(range(0,pdf_len,step))
# Loop through the pdf pages
for ind,val in enumerate(page_numbers):
# Check if the index is last in the given page numbers
# If the index is not the last one, carry on with the If block.
if(ind+1 != len(page_numbers)):
# Initialize the PDF Writer
output_1 = PdfFileWriter()
# Loop through the pdf pages starting from the value of current index till the value of next index
# Ex : page numbers = [0,2,4,6,8]
# If the current index is 0, loop from 1st page till the 2nd page in the pdf doc.
for page in range(page_numbers[ind], page_numbers[ind+1]):
# Get the data from the given page number
page_data = input_pdf.getPage(page)
# Add the page data to the pdf_writer
output_1.addPage(page_data)
# Frame the output file name
output_1_filename = '{}_page_{}.pdf'.format(fname, page + 1)
# Write the output content to the file and save it.
self.write_to_file(output_1_filename, output_1)
else:
output_final = PdfFileWriter()
output_final_filename = "Last_Pages"
# Loop through the pdf pages starting from the value of current index till the last page of the pdf doc.
# Ex : page numbers = [0,2,4,6,8]
# If the current index is 8, loop from 8th page till the last page in the pdf doc.
for page in range(page_numbers[ind], pdf_len):
# Get the data from the given page number
page_data = input_pdf.getPage(page)
# Add the page data to the pdf_writer
output_final.addPage(page_data)
# Frame the output file name
output_final_filename = '{}_page_{}.pdf'.format(fname, page + 1)
# Write the output content to the file and save it.
self.write_to_file(output_final_filename,output_final)
I am very new to Python, and I am trying to break some legal documents into sections for export into SQL. I need to do two things:
Define the section numbers by the table of contents, and
Break up the document given the defined section numbers
The table of contents lists section numbers: 1.1, 1.2, 1.3, etc.
Then the document itself is broken up by those section numbers:
1.1 "...Text...",
1.2 "...Text...",
1.3 "...Text...", etc.
Similar to the chapters of a book, but delimited by ascending decimal numbers.
I have the document parsed using Tika, and I've been able to create a list of sections with some basic regex:
import tika
import re
from tika import parser
parsed = parser.from_file('test.pdf')
content = (parsed["content"])
headers = re.findall("[0-9]*[.][0-9]",content)
Now I need to do something like this:
splitsections = content.split() by headers
var_string = ', '.join('?' * len(splitsections))
query_string = 'INSERT INTO table VALUES (%s);' % var_string
cursor.execute(query_string, splitsections)
Sorry if all this is unclear. Still very new to this.
Any help you can provide would be most appreciated.
Everything tested except the last part with DB. Also the code can be improved, but this is another task. The main task is done.
In the list split_content there are all pieces of info you wanted (i.e. the text between 2.1 and 2.2, then 2.2 and 2.3, and so on, EXCLUDING num+name of sections itself (i.e. excluding 2.1 Continuation, 2.2 Name and so on).
I replaced tika by PyPDF2, as tika does not provide instruments needed for this task (i.e. I did not find how to provide the num of page I need and get its content).
def get_pdf_content(pdf_path,
start_page_table_contents, end_page_table_contents,
first_parsing_page, last_phrase_to_stop):
"""
:param pdf_path: Full path to the PDF file
:param start_page_table_contents: The page where the "Contents table" starts
:param end_page_table_contents: The page where the "Contents Table" ends
(i.e. the number of the page where Contents Table ENDs, i.e. not the next one)
:param first_parsing_page: The 1st page where we need to start data grabbing
:param last_phrase_to_stop: The phrase that tells the code where to stop grabbing.
The phrase must match exactly what is written in PDF.
This phrase will be excluded from the grabbed data.
:return:
"""
# ======== GRAB TABLE OF CONTENTS ========
start_page = start_page_table_contents
end_page = end_page_table_contents
table_of_contents_page_nums = range(start_page-1, end_page)
sections_of_articles = [] # ['2.1 Continuation', '2.2 Name', ... ]
open_file = open(pdf_path, "rb")
pdf = PyPDF2.PdfFileReader(open_file)
for page_num in table_of_contents_page_nums:
page_content = pdf.getPage(page_num).extractText()
page_sections = re.findall("[\d]+[.][\d][™\s\w;,-]+", page_content)
for section in page_sections:
cleared_section = section.replace('\n', '').strip()
sections_of_articles.append(cleared_section)
# ======== GRAB ALL NECESSARY CONTENT (MERGE ALL PAGES) ========
total_num_pages = pdf.getNumPages()
parsing_pages = range(first_parsing_page-1, total_num_pages)
full_parsing_content = '' # Merged pages
for parsing_page in parsing_pages:
page_content = pdf.getPage(parsing_page).extractText()
cleared_page = page_content.replace('\n', '')
# Remove page num from the start of "page_content"
# Covers the case with the page 65, 71 and others when the "page_content" starts
# with, for example, "616.6 Liability to Partners. (a) It is understood that"
# i.e. "61" is the page num and "6.6 Liability ..." is the section data
already_cleared = False
first_50_chars = cleared_page[:51]
for section in sections_of_articles:
if section in first_50_chars:
indx = cleared_page.index(section)
cleared_page = cleared_page[indx:]
already_cleared = True
break
# Covers all other cases
if not already_cleared:
page_num_to_remove = re.match(r'^\d+', cleared_page)
if page_num_to_remove:
cleared_page = cleared_page[len(str(page_num_to_remove.group(0))):]
full_parsing_content += cleared_page
# ======== BREAK ALL CONTENT INTO PIECES ACCORDING TO TABLE CONTENTS ========
split_content = []
num_sections = len(sections_of_articles)
for num_section in range(num_sections):
start = sections_of_articles[num_section]
# Get the last piece, i.e. "11.16 FATCA" (as there is no any "end" section after "11.16 FATCA", so we cant use
# the logic like "grab info between sections 11.1 and 11.2, 11.2 and 11.3 and so on")
if num_section == num_sections-1:
end = last_phrase_to_stop
else:
end = sections_of_articles[num_section + 1]
content = re.search('%s(.*)%s' % (start, end), full_parsing_content).group(1)
cleared_piece = content.replace('™', "'").strip()
if cleared_piece[0:3] == '. ':
cleared_piece = cleared_piece[3:]
# There are few appearances of "[Signature Page Follows]", as a "last_phrase_to_stop".
# We need the text between "11.16 FATCA" and the 1st appearance of "[Signature Page Follows]"
try:
indx = cleared_piece.index(end)
cleared_piece = cleared_piece[:indx]
except ValueError:
pass
split_content.append(cleared_piece)
# ======== INSERT TO DB ========
# Did not test this section
for piece in split_content:
var_string = ', '.join('?' * len(piece))
query_string = 'INSERT INTO table VALUES (%s);' % var_string
cursor.execute(query_string, parts)
How to use: (one of the possible way):
1) Save the code above in my_pdf_code.py
2) In the python shell:
import path.to.my_pdf_code as the_code
the_code.get_pdf_content('/home/username/Apollo_Investment_Fund_VIII_LPA_S1.pdf', 2, 4, 24, '[Signature Page Follows]')
I recently upgraded my Celery installation to 4.0. After a few days of wrestling with the upgrade process, I finally got it to work... sort of. Some tasks will return, but the final task will not.
I have a class, SFF, that takes in and parses a file:
# Constructor with I/O file
def __init__(self, file):
# File data that's gonna get used a lot
sffDescriptor = file.fileno()
fileName = abspath(file.name)
# Get the pointer to the file
filePtr = mmap.mmap(sffDescriptor, 0, flags=mmap.MAP_SHARED, prot=mmap.PROT_READ)
# Get the header info
hdr = filePtr.read(HEADER_SIZE)
self.header = SFFHeader._make(unpack(HEADER_FMT, hdr))
# Read in the palette maps
print self.header.onDemandDataSize
print self.header.onLoadDataSize
palMapsResult = getPalettes.delay(fileName, self.header.palBankOff - HEADER_SIZE, self.header.onDemandDataSize, self.header.numPals)
# Read the sprite list nodes
nodesStart = self.header.sprListOff
nodesEnd = self.header.palBankOff
print nodesEnd - nodesStart
sprNodesResult = getSprNodes.delay(fileName, nodesStart, nodesEnd, self.header.numSprites)
# Get palette data
self.palettes = palMapsResult.get()
# Get sprite data
spriteNodes = sprNodesResult.get()
# TESTING
spritesResultSet = ResultSet([])
numSpriteNodes = len(spriteNodes)
# Split the nodes into chunks of size 32 elements
for x in xrange(0, numSpriteNodes, 32):
spritesResult = getSprites.delay(spriteNodes, x, x+32, fileName, self.palettes, self.header.palBankOff, self.header.onDemandDataSizeTotal)
spritesResultSet.add(spritesResult)
break # REMEMBER TO REMOVE FOR ENTIRE SFF
self.sprites = spritesResultSet.join_native()
It doesn't matter if it's a single task that returns the entire spritesResult, or if I split it using a ResultSet, the outcome is always the same: the Python console I'm using just hangs at either spritesResultSet.join_native() or spritesResult.get() (depending on how I format it).
Here is the task in question:
#task
def getSprites(nodes, start, end, fileName, palettes, palBankOff, onDemandDataSizeTotal):
sprites = []
with open(fileName, "rb") as file:
sffDescriptor = file.fileno()
sffData = mmap.mmap(sffDescriptor, 0, flags=mmap.MAP_SHARED, prot=mmap.PROT_READ)
for node in nodes[start:end]:
sprListNode = dict(SprListNode._make(node)._asdict()) # Need to convert it to a dict since values may change.
#print node
#print sprListNode
# If it's a linked sprite, the data length is 0, so get the linked index.
if sprListNode['dataLen'] == 0:
sprListNodeTemp = SprListNode._make(nodes[sprListNode['index']])
sprListNode['dataLen'] = sprListNodeTemp.dataLen
sprListNode['dataOffset'] = sprListNodeTemp.dataOffset
sprListNode['compression'] = sprListNodeTemp.compression
# What does the offset need to be?
dataOffset = sprListNode['dataOffset']
if sprListNode['loadMode'] == 0:
dataOffset += palBankOff #- HEADER_SIZE
elif sprListNode['loadMode'] == 1:
dataOffset += onDemandDataSizeTotal #- HEADER_SIZE
#print sprListNode
# Seek to the data location and "read" it in. First 4 bytes are just the image length
start = dataOffset + 4
end = dataOffset + sprListNode['dataLen']
#sffData.seek(start)
compressedSprite = sffData[start:end]
# Create the sprite
sprite = Sprite(sprListNode, palettes[sprListNode['palNo']], np.fromstring(compressedSprite, dtype=np.uint8))
sprites.append(sprite)
return json.dumps(sprites, cls=SpriteJSONEncoder)
I know it reaches the return statement, because if I put a print right above it, it will print in the Celery window. I also know that the task is running to completion because I get the following message from the worker:
[2016-11-16 00:03:33,639: INFO/PoolWorker-4] Task framedatabase.tasks.getSprites[285ac9b1-09b4-4cf1-a251-da6212863832] succeeded in 0.137236133218s: '[{"width": 120, "palNo": 30, "group": 9000, "xAxis": 0, "yAxis": 0, "data":...'
Here are my celery settings in settings.py:
# Celery settings
BROKER_URL='redis://localhost:1717/1'
CELERY_RESULT_BACKEND='redis://localhost:1717/0'
CELERY_IGNORE_RESULT=False
CELERY_IMPORTS = ("framedatabase.tasks", )
... and my celery.py:
from __future__ import absolute_import
import os
from celery import Celery
# set the default Django settings module for the 'celery' program.
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'framedatabase.settings')
from django.conf import settings # noqa
app = Celery('framedatabase', backend='redis://localhost:1717/1', broker="redis://localhost:1717/0",
include=['framedatabase.tasks'])
# Using a string here means the worker will not have to
# pickle the object when using Windows.
app.config_from_object('django.conf:settings', namespace='CELERY')
app.autodiscover_tasks()
#app.task(bind=True)
def debug_task(self):
print('Request: {0!r}'.format(self.request))
Found the problem. Apparently it was leading to deadlock as mentioned in the section "Avoid launching synchronous subtasks" in the Celery documentation here: http://docs.celeryproject.org/en/latest/userguide/tasks.html#tips-and-best-practices
So I got rid of the line:
sprNodesResult.get()
And changed the final result to a chain:
self.sprites = chain(getSprNodes.s(fileName, nodesStart, nodesEnd, self.header.numSprites),
getSprites.s(0,32,fileName,self.palettes,self.header.palBankOff,self.header.onDemandDataSizeTotal))().get()
And it works! Now I just have to find a way to split this the way I want!
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])
I want to know if it is possible to import data of attitude and position (roll/pitch/yaw & xyz) from a comma separated file to Blender?
I recorded data from a little RC car and I want to represent its movement in a 3D world.
I have timestamps too, so if there's a way to animated the movement of the object it'll be superb!!
Any help will be greatly appreciated!!
Best Regards.
A slight modifcation, making use of the csv module
import bpy
import csv
position_vectors = []
filepath = "C:\\Work\\position.log"
csvfile = open(filepath, 'r', newline='')
ofile = csv.reader(csvfile, delimiter=',')
for row in ofile:
position_vectors.append(tuple([float(i) for i in row]))
csvfile.close()
This will get your points into Blender. Note the delimiter parameter in csv.reader, change that accordingly. With a real example file of your RC car we could provide a more complete solution.
For blender v2.62:
If you have a file "positions.log" looking like:
-8.691985196313894e-002; 4.119284642631801e-001; -5.832147659661263e-001
1.037146774956164e+000; 8.137243553005405e-002; -5.703274929662892e-001
-3.602584527944123e-001; 8.378614512537046e-001; 2.615265921163826e-001
6.266465707681335e-001; -1.128416901202341e+000; -1.664644365541639e+000
3.327523280880091e-001; 4.488553740582839e-001; -2.449449085462368e+000
-7.311567199869298e-001; -1.860587923723032e+000; -1.297179602213110e+000
-7.453603745688361e-003; 4.770473577895327e-001; -2.319515785100494e+000
1.935170866863264e-001; -2.010280476717868e+000; 3.748000986190077e-001
5.201529166915653e-001; 3.952972788761738e-001; 1.658581747430548e+000
4.719198263774027e-001; 1.526020825619557e+000; 3.187088567866725e-002
you can read it with this python script in blender (watch out for the indentation!)
import bpy
from mathutils import *
from math import *
from bpy.props import *
import os
import time
# Init
position_vector = []
# Open file
file = open("C:\\Work\\position.log", "r")
# Loop over line in file
for line in file:
# Split line at ";"
splittet_line = line.split(";")
# Append new postion
position_vector.append(
Vector((float(splittet_line[0]),
float(splittet_line[1]),
float(splittet_line[2]))))
# Close file
file.close()
# Get first selected object
selected_object = bpy.context.selected_objects[0]
# Get first selected object
for position in position_vector:
selected_object.location = position
This reads the file and updates the position of the first selected object accordingly. Way forward: What you have to find out is how to set the keyframes for the animation...
Consider this python snippet to add to the solutions above
obj = bpy.context.object
temporalScale=bpy.context.scene.render.fps
for lrt in locRotArray:
obj.location = (lrt[0], lrt[1], lrt[2])
# radians, and do you want XYZ, or ZYX?
obj.rotation_euler = (lrt[3], lrt[4], lrt[5])
time = lrt[6]*temporalScale
obj.keyframe_insert(data_path="location", frame=time)
obj.keyframe_insert(data_path="rotation_euler", frame=time)
I haven't tested it, but it will probably work, and gets you started.
With a spice2xyzv file as input file. The script writed by "Mutant Bob" seems to work.
But the xyz velocity data are km/s not euler angles, I think, and the import does not work for the angles.
# Records are <jd> <x> <y> <z> <vel x> <vel y> <vel z>
# Time is a TDB Julian date
# Position in km
# Velocity in km/sec
2456921.49775 213928288.518 -446198013.001 -55595492.9135 6.9011736 15.130842 0.54325805
Is there a solution to get them in Blender? Should I convert velocity angle to euler, is that possible in fact?
I use this script :
import bpy
from mathutils import *
from math import *
from bpy.props import *
import os
import time
# Init
position_vector = []
# Open file
file = open("D:\\spice2xyzv\\export.xyzv", "r")
obj = bpy.context.object
temporalScale=bpy.context.scene.render.fps
for line in file:
# Split line at ";"
print("line = %s" % line)
line = line.replace("\n","")
locRotArray = line.split(" ")
print("locRotArray = %s" % locRotArray )
#for lrt in locRotArray:
print(locRotArray[1])
obj.location = (float(locRotArray[1]), float(locRotArray[2]), float(locRotArray[3]))
# radians, and do you want XYZ, or ZYX?
obj.rotation_euler = (float(locRotArray[4]), float(locRotArray[5]), float(locRotArray[5]))
time = float(locRotArray[0])*temporalScale
print("time = %s" % time)
obj.keyframe_insert(data_path="location", frame=time)
obj.keyframe_insert(data_path="rotation_euler", frame=time)