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This is a simple library for reading and writing .tps files as created and used by the tpsDig landmarking tool created by F. James Rohlf. https://life.bio.sunysb.edu/morph/

Project description

This is a simple library for reading and writing .tps files as created and used by the tpsDig landmarking tool created by F. James Rohlf. https://life.bio.sunysb.edu/morph/

Installation

The primary way to install is from pip:

pip install py_tps

Installation from source is managed via poetry. https://pypi.org/project/poetry/ Source can be obtained from https://gitlab.com/ryan-feather/py_tps

To install, first install poetry.

Note for conda users

In order to use a conda environment with poetry, you must first configure poetry to use your conda environment and not create a new virtualenv environment. Example:

poetry config settings.virtualenvs.path $CONDA_ENV_PATH
poetry config settings.virtualenvs.create 0

Then run:

poetry install
poetry build
cd dist
pip install *.whl

Usage

from py_tps import TPSFile, TPSImage, TPSCurve, TPSPoints
import numpy as np

# construct and write
# numpy is used for numeric data
points = TPSPoints(np.asarray([[33,44],
                               [44,45]]))
curve = TPSCurve(points)
image = TPSImage('T1.JPG', curves=[curve], id_number=0, comment="This is a test", scale=0.0045)
tps_file = TPSFile([image]) # can have many images, but here we do just one
tps_file.write_to_file('TestFile.TPS')

Creates a file with the contents:

LM=0
CURVES=1
POINTS=2
33 44
44 45
IMAGE=T1.JPG
ID=0
COMMENT=This is a test
SCALE=0.0045

Now to read:

tps_file_in =TPSFile.read_file('TestFile.TPS')
# now can access images list, and so on.  Attributes have the same names as they do in the objects above.
print(tps_file.images[0].image) # T1.JPG
print(tps_file.images[0].curves[0].tps_points.points) # [[33,44],[44,45]]

Landmarks can be set instead of or with curves. If we instead do:

image = TPSImage('T1.JPG', landmarks=points, id_number=0, comment="This is a test", scale=0.0045)

It creates the file with contents:

LM=2
33 44
44 45
IMAGE=T1.JPG
ID=0
COMMENT=This is a test
SCALE=0.0045

Project details


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