plyfile 0.7.2

PLY file reader/writer

Welcome to the plyfile Python module, which provides a simple facility for reading and writing ASCII and binary PLY files.

The PLY format is documented elsewhere.

Installation

Dependencies

• python2 >= 2.7 or python3
• numpy >= 1.8

Note: numpy 1.9 before version 1.9.2 has a bug that breaks byte swapping by manipulating the byte_order field of a PlyData instance. As a workaround, you can manually byte-swap your arrays using el.data = el.data.byteswap().newbyteorder() in addition to changing the byte_order attribute.

Optional dependencies

• setuptools (for installation via setup.py)
• tox (for test suite)
• py.test and py (for test suite)

Installing plyfile

Quick way:

pip install plyfile

Or clone the repository and run from the project root:

python setup.py install

Or just copy plyfile.py into your GPL-compatible project.

Running test suite

Preferred (more comprehensive; requires tox and setuptools):

tox -v

Alternate (requires py.test and py):

py.test test -v

Usage

Both deserialization and serialization of PLY file data is done through PlyData and PlyElement instances.

>>> from plyfile import PlyData, PlyElement

For the code examples that follow, assume the file tet.ply contains the following text:

ply
format ascii 1.0
comment single tetrahedron with colored faces
element vertex 4
comment tetrahedron vertices
property float x
property float y
property float z
element face 4
property list uchar int vertex_indices
property uchar red
property uchar green
property uchar blue
end_header
0 0 0
0 1 1
1 0 1
1 1 0
3 0 1 2 255 255 255
3 0 2 3 255 0 0
3 0 1 3 0 255 0
3 1 2 3 0 0 255

(This file is available under the examples directory.)

Reading a PLY file

>>> plydata = PlyData.read('tet.ply')

or

>>> with open('tet.ply', 'rb') as f:
...     plydata = PlyData.read(f)

The static method PlyData.read returns a PlyData instance, which is plyfile's representation of the data in a PLY file. A PlyData instance has an attribute elements, which is a list of PlyElement instances, each of which has a data attribute which is a numpy structured array containing the numerical data. PLY file elements map onto numpy structured arrays in a pretty obvious way. For a list property in an element, the corresponding numpy field type is object, with the members being numpy arrays (see the vertex_indices example below).

Concretely:

>>> plydata.elements[0].name
'vertex'
>>> plydata.elements[0].data[0]
(0.0, 0.0, 0.0)
>>> plydata.elements[0].data['x']
array([ 0.,  0.,  1.,  1.], dtype=float32)
>>> plydata['face'].data['vertex_indices'][0]
array([0, 1, 2], dtype=int32)

For convenience, elements and properties can be looked up by name:

>>> plydata['vertex']['x']
array([ 0.,  0.,  1.,  1.], dtype=float32)

and elements can be indexed directly without explicitly going through the data attribute:

>>> plydata['vertex'][0]
(0.0, 0.0, 0.0)

The above expression is equivalent to plydata['vertex'].data[0].

PlyElement instances also contain metadata:

>>> plydata.elements[0].properties
(PlyProperty('x', 'float'), PlyProperty('y', 'float'),
 PlyProperty('z', 'float'))
>>> plydata.elements[0].count
4

PlyProperty and PlyListProperty instances are used internally as a convenient intermediate representation of PLY element properties that can easily be serialized to a PLY header (using str) or converted to numpy-compatible type descriptions (via the dtype method). It's not extremely common to manipulate them directly, but if needed, the property metadata of an element can be accessed as a tuple via the properties attribute (as illustrated above) or looked up by name:

>>> plydata.elements[0].ply_property('x')
PlyProperty('x', 'float')

Many (but not necessarily all) types of malformed input files will raise PlyParseError when PlyData.read is called. The string value of the PlyParseError instance (as well as attributes element, row, and prop) provides additional context for the error if applicable.

Creating a PLY file

The first step is to get your data into numpy structured arrays. Note that there are some restrictions: generally speaking, if you know the types of properties a PLY file element can contain, you can easily deduce the restrictions. For example, PLY files don't contain 64-bit integer or complex data, so these aren't allowed.

For convenience, non-scalar fields are allowed; they will be serialized as list properties. For example, when constructing a "face" element, if all the faces are triangles (a common occurrence), it's okay to have a "vertex_indices" field of type 'i4' and shape (3,) instead of type object and shape (). However, if the serialized PLY file is read back in using plyfile, the "vertex_indices" property will be represented as an object-typed field, each of whose values is an array of type 'i4' and length 3. The reason is simply that the PLY format provides no way to find out that each "vertex_indices" field has length 3 without actually reading all the data, so plyfile has to assume that this is a variable-length property. However, see below (and examples/plot.py) for an easy way to recover a two-dimensional array from a list property.

For example, if we wanted to create the "vertex" and "face" PLY elements of the tet.ply data directly as numpy arrays for the purpose of serialization, we could do (as in test/test.py):

>>> vertex = numpy.array([(0, 0, 0),
...                       (0, 1, 1),
...                       (1, 0, 1),
...                       (1, 1, 0)],
...                      dtype=[('x', 'f4'), ('y', 'f4'),
...                             ('z', 'f4')])
>>> face = numpy.array([([0, 1, 2], 255, 255, 255),
...                     ([0, 2, 3], 255,   0,   0),
...                     ([0, 1, 3],   0, 255,   0),
...                     ([1, 2, 3],   0,   0, 255)],
...                    dtype=[('vertex_indices', 'i4', (3,)),
...                           ('red', 'u1'), ('green', 'u1'),
...                           ('blue', 'u1')])

Once you have suitably structured array, the static method PlyElement.describe can then be used to create the necessary PlyElement instances:

>>> el = PlyElement.describe(some_array, 'some_name')

or

>>> el = PlyElement.describe(some_array, 'some_name',
...                          comments=['comment1',
...                                    'comment2'])

Note that there's no need to create PlyProperty instances explicitly. This is all done behind the scenes by examining some_array.dtype.descr. One slight hiccup here is that variable-length fields in a numpy array (i.e., our representation of PLY list properties) must have a type of object, so the types of the list length and values in the serialized PLY file can't be obtained from the array's dtype attribute alone. For simplicity and predictability, the length defaults to 8-bit unsigned integer, and the value defaults to 32-bit signed integer, which covers the majority of use cases. Exceptions must be stated explicitly:

>>> el = PlyElement.describe(some_array, 'some_name',
...                          val_dtypes={'some_property': 'f8'},
...                          len_dtypes={'some_property': 'u4'})

Now you can instantiate PlyData and serialize:

>>> PlyData([el]).write('some_binary.ply')
>>> PlyData([el], text=True).write('some_ascii.ply')

# Force the byte order of the output to big-endian, independently of
# the machine's native byte order
>>> PlyData([el],
...         byte_order='>').write('some_big_endian_binary.ply')

# Use a file object.  Binary mode is used here, which will cause
# Unix-style line endings to be written on all systems.
>>> with open('some_ascii.ply', mode='wb') as f:
...     PlyData([el], text=True).write(f)

Miscellaneous

Comments

Header comments are supported:

>>> ply = PlyData([el], comments=['header comment'])
>>> ply.comments
['header comment']

As of version 0.3, "obj_info" comments are supported as well:

>>> ply = PlyData([el], obj_info=['obj_info1', 'obj_info2'])
>>> ply.obj_info
['obj_info1', 'obj_info2']

When written, they will be placed after regular comments after the "format" line.

Comments can have leading whitespace, but trailing whitespace may be stripped and should not be relied upon. Comments may not contain embedded newlines.

Getting a two-dimensional array from a list property

The PLY format provides no way to assert that all the data for a given list property is of the same length, yet this is a relatively common occurrence. For example, all the "vertex_indices" data on a "face" element will have length three for a triangular mesh. In such cases, it's usually much more convenient to have the data in a two-dimensional array, as opposed to a one-dimensional array of type object. Here's a pretty easy way to obtain a two dimensional array, assuming we know the row length in advance:

>>> plydata = PlyData.read('tet.ply')
>>> tri_data = plydata['face'].data['vertex_indices']
>>> triangles = numpy.vstack(tri_data)

Instance mutability

A plausible code pattern is to read a PLY file into a PlyData instance, perform some operations on it, possibly modifying data and metadata in place, and write the result to a new file. This pattern is partially supported. As of version 0.4, the following in-place mutations are supported:

• Modifying numerical array data only.
• Assigning directly to a PlyData instance's elements.
• Switching format by changing the text and byte_order attributes of a PlyData instance. This will switch between ascii, binary_little_endian, and binary_big_endian PLY formats.
• Modifying a PlyData instance's comments and obj_info, and modifying a PlyElement instance's comments.
• Assigning to an element's data. Note that the property metadata in properties is not touched by this, so for every property in the properties list of the PlyElement instance, the data array must have a field with the same name (but possibly different type, and possibly in different order). The array can have additional fields as well, but they won't be output when writing the element to a PLY file. The properties in the output file will appear as they are in the properties list. If an array field has a different type than the corresponding PlyProperty instance, then it will be cast when writing.
• Assigning directly to an element's properties. Note that the data array is not touched, and the previous note regarding the relationship between properties and data still applies: the field names of data must be a subset of the property names in properties, but they can be in a different order and specify different types.
• Changing a PlyProperty or PlyListProperty instance's val_dtype or a PlyListProperty instance's len_dtype, which will perform casting when writing.

Modifying the name of a PlyElement, PlyProperty, or PlyListProperty instance is not supported and will raise an error. To rename a property of a PlyElement instance, you can remove the property from properties, rename the field in data, and re-add the property to properties with the new name by creating a new PlyProperty or PlyListProperty instance:

>>> from plyfile import PlyProperty, PlyListProperty
>>> face = plydata['face']
>>> face.properties = ()
>>> face.data.dtype.names = ['idx', 'r', 'g', 'b']
>>> face.properties = (PlyListProperty('idx', 'uchar', 'int'),
...                    PlyProperty('r', 'uchar'),
...                    PlyProperty('g', 'uchar'),
...                    PlyProperty('b', 'uchar'))

Note that it is always safe to create a new PlyElement or PlyData instance instead of modifying one in place, and this is the recommended style:

>>> # Recommended:
>>> plydata = PlyData([plydata['face'], plydata['vertex']],
                      text=False, byte_order='<')

>>> # Also supported:
>>> plydata.elements = [plydata['face'], plydata['vertex']]
>>> plydata.text = False
>>> plydata.byte_order = '<'
>>> plydata.comments = []
>>> plydata.obj_info = []

Objects created by this library don't claim ownership of the other objects they refer to, which has implications for both styles (creating new instances and modifying in place). For example, a single PlyElement instance can be contained by multiple PlyData instances, but modifying that instance will then affect all of those containing PlyData instances.

Design philosophy and rationale

At the time that I wrote this, I didn't know of any simple and self-contained Python PLY file module using numpy as its data representation medium. Considering the increasing prevalence of Python as a tool for scientific programming with NumPy as the lingua franca for numerical data, such a module seemed desirable; hence, plyfile was born.

Familiarity

I opted to use existing Python and NumPy constructs whenever they matched the data. Thus, the elements attribute of a PlyData instance is simply a list of PlyElement instances, and the data attribute of a PlyElement instance is a numpy array, and a list property field of a PLY element datum is referred to in the data attribute by a type of object with the value being another numpy array, etc. In the last case, this is certainly not the most-efficient in-memory representation of the data, since it contains a lot of indirection. However, it is arguably the most obvious and natural unless NumPy adds explicit support for "ragged" arrays in its type system. The design goal was to represent data in a form familiar to users of numpy.

Simplicity

When the two were at odds, I decided to favor simplicity over power or user-friendliness. Thus, list property types in PlyElement.describe always default to the same, rather than, say, being obtained by looking at an array element. (Which element? What if the array has length zero? Whatever default we could choose in that case could lead to subtle edge-case bugs if the user isn't vigilant.) Also, all input and output is done in "one shot": all the arrays must be created up front rather than being processed in a streaming fashion. (That said, I have nothing against streamability, and I considered it at one point. I decided against it for now in order to have a consistent and maintainable interface at least for the first usable version.)

Interpretation issues

There doesn't seem to be a single complete and consistent description of the PLY format. Even the "authoritative" Ply.txt by Greg Turk has some issues.

Comment placement

Where can comments appear in the header? It appears that in all the "official" examples, all comments immediately follow the "format" line, but the language of the document neither places any such restrictions nor explicitly allows comments to be placed anywhere else. Thus, it isn't clear whether comments can appear anywhere in the header or must immediately follow the "format" line. At least one popular reader of PLY files chokes on comments before the "format" line. plyfile accepts comments anywhere in the header in input but only places them in a few limited places in output, namely immediately after "format" and "element" lines.

Element and property names

Another ambiguity is names: what strings are allowed as PLY element and property names? plyfile accepts as input any name that doesn't contain spaces, but this is surely too generous. This may not be such a big deal, though: although names are theoretically arbitrary, in practice, the majority of PLY element and property names probably come from a small finite set ("face", "x", "nx", "green", etc.).

Property syntax

A more serious problem is that the PLY format specification appears to be inconsistent regarding the syntax of property definitions. In some examples, it uses the syntax

property {type} {name}

and in others,

property {name} {type}

plyfile only supports the former, which appears to be standard de facto.

Header line endings

The specification explicitly states that lines in the header must end with carriage returns, but this rule doesn't seem to be followed by anyone, including the C-language PLY implementation by Greg Turk, the author of the format. Here, we stick to common practice and output Unix-style line endings (with no carriage returns) but accept any line ending style in input files.

More examples

Examples beyond the scope of this document and the tests are in the examples directory.

Credits

Author: Darsh Ranjan

License

This software is released under the terms of the GNU General Public License, version 3. See the file COPYING for details.