Implement initializers

Purge

README.md

@@ -15,7 +15,15 @@ Nevertheless, this library focuses on simplicity, readability and accessibility,
 
 ------------------------
 
+## Installation
+
+- Installation from PyPI: `pip install pypcl`
+- Installation from source: `python setup.py install`
+- Installation from source in-place: `python setup.py develop`
+
+------------------------
+
 ## Notes
-The cython doesn't support a template technique which is similar to ["covariant"](https://en.wikipedia.org/wiki/Covariance_and_contravariance_(computer_science)) in its template support, so the code which need this technique is not wrapped or header-provided as stated above.
+The cython doesn't support a template technique similar to ["covariant"](https://en.wikipedia.org/wiki/Covariance_and_contravariance_(computer_science)) in its template support, so the code which need this technique is not wrapped or header-provided as stated above.
 
 The library is under heavy construction, thus do not use it in productive codes. However, playing with it is totally welcome now, and it will be great to receive your issues, suggestions and pull requests!~

TODO.md

@@ -3,3 +3,5 @@
 - [ ] Add conversion between numpy array and Eigen objects
 - [ ] Migrate original implementations of pypcl
 - [ ] Fix TODOs in the code
+- [ ] Instantiate template classes to given point-type (e.g. PointXYZ)
+- [ ] Support organized point cloud

pcl/CMakeLists.txt

@@ -29,3 +29,5 @@ add_library(Visualizer MODULE ${Visualizer})
 target_link_libraries(Visualizer ${PCL_LIBRARIES})
 python_extension_module(Visualizer)
 install(TARGETS Visualizer LIBRARY DESTINATION pcl)
+
+add_subdirectory(io)

pcl/PointCloud.pyx

@@ -1,19 +1,16 @@
-from cython.operator cimport dereference as deref
 from libc.stdint cimport uint8_t
 from libcpp cimport bool
 from libcpp.string cimport string
-from cpython cimport bool as PyBool
+from cython.operator cimport dereference as deref
+import sys
 import numpy as np
 cimport numpy as np
-import warnings
 
 from pcl._boost.smart_ptr cimport make_shared
 from .ros import ros_exist, ros_error
 if ros_exist: from pcl.ros cimport from_msg_cloud, to_msg_cloud
 from pcl.common.conversions cimport toPCLPointCloud2, fromPCLPointCloud2
 from pcl.common.point_cloud cimport PointCloud as cPC
-from pcl.io.pcd_io cimport loadPCDFile, savePCDFile
-from pcl.io.ply_io cimport loadPLYFile, savePLYFile
 from pcl.PointField cimport PointField, _FIELD_TYPE_MAPPING
 
 # XXX: unordered_map[string, vector[(string, uint8_t, uint32_t)]]
@@ -52,31 +49,32 @@ cdef string _check_dtype_compatible(np.dtype dtype):
         tuple data_fields
         tuple data_dtypes
 
-    for name, typetuple in _POINT_TYPE_MAPPING:
-        builtin_fields = tuple(name for name,_,_ in typetuple)
-        builtin_dtypes = tuple(_FIELD_TYPE_MAPPING[typeid] for _,typeid,_ in typetuple)
+    for name, typetuple in _POINT_TYPE_MAPPING.items():
+        builtin_fields = tuple(name.decode('ascii') for name,_,_ in typetuple)
+        builtin_dtypes = tuple(_FIELD_TYPE_MAPPING[typeid][0] for _,typeid,_ in typetuple)
         data_fields = dtype.names
-        data_dtypes = tuple(_parse_single_dtype(dtype[name]).encode('ascii') for name in dtype.names)
+        data_dtypes = tuple(_parse_single_dtype(dtype[name]) for name in dtype.names)
         if builtin_fields == data_fields and builtin_dtypes == data_dtypes:
             return name
     return b""
 
-cdef bool _is_not_record_array(np.ndarray array):
-    return array.dtype.isbuiltin
+cdef inline bool _is_not_record_array(np.ndarray array):
+    # https://github.com/numpy/numpy/blob/master/numpy/core/_dtype.py#L107
+    return array.dtype.fields is None
 
 cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
     def __cinit__(self):
         self._origin = Vector4f.Zero()
         self._orientation = Quaternionf.Identity()
 
-    def __init__(self, data=None, point_type=None, copy=False):
+    def __init__(self, data=None, point_type='XYZ'):
         """
         Initialize a point cloud
 
         # Parameters
         - data: point cloud data, can be a PointCloud or a numpy array. If the dimension of input
             is 3, then it will be considered as dense point cloud with dimensions (height,
-            width, data)
+            width, data). The input data will always be copied.
         - point_type: if normal numpy array is given, the type of point should be specified 
             if you are using other PCL components on it. The valid point_types are:
             - Intensity
@@ -107,24 +105,33 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
                 from_msg_cloud(data, deref(self._ptr))
                 initialized = True
         if isinstance(data, PointCloud):
-            # TODO: support non-copy instantiation
-            self._ptr = (<PointCloud>data)._ptr
+            self._ptr = make_shared[PCLPointCloud2]()
+            self.ptr()[0] = (<PointCloud>data).ptr()[0] # copy struct
             self._origin = (<PointCloud>data)._origin
             self._orientation = (<PointCloud>data)._orientation
             self._ptype = (<PointCloud>data)._ptype
             initialized = True
         if isinstance(data, (list, tuple)):
-            # TODO: support different dtype
-            data = np.ndarray(data)
+            if point_type == None:
+                raise ValueError('Point type should be specified when normal array is inputed')
+            self._ptype = point_type.upper().encode('ascii')
+            if <bytes>(self._ptype) not in _POINT_TYPE_MAPPING:
+                raise TypeError('Unsupported point type!')
+
+            ndtype = []
+            byte_order = '>' if sys.byteorder == 'big' else '<'
+            for name, typeid, count in _POINT_TYPE_MAPPING[self._ptype]:
+                ndtype.append((name.decode('ascii'),
+                    str(count) + byte_order + _FIELD_TYPE_MAPPING[typeid][0]))
+            data = np.array(data, dtype=ndtype)
         if isinstance(data, np.ndarray):
+            self._ptr = make_shared[PCLPointCloud2]()
             # matrix order detection
             if not data.flags.c_contiguous:
                 data = data.ascontiguousarray()
-                if copy: warnings.warn('The matrix order is inconsistent, data copy is forced!')
 
-            # TODO: support copying instantiation
             # datatype interpreting
-            if _is_not_record_array(data): # normal array
+            if _is_not_record_array(data): # [normal array]
                 # data shape interpreting
                 if len(data.shape) < 2 or len(data.shape) > 3:
                     raise ValueError("Unrecognized input data shape")
@@ -143,7 +150,7 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
                     raise ValueError('Point type should be specified when normal array is inputed')
                 self._ptype = point_type.upper().encode('ascii')
                 if <bytes>(self._ptype) not in _POINT_TYPE_MAPPING:
-                    warnings.warn('Unsupported point type!')
+                    raise TypeError('Unsupported point type!')
                 else:
                     # field consensus check
                     if data.shape[-1] != len(_POINT_TYPE_MAPPING[self._ptype]):
@@ -156,7 +163,14 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
                         raise ValueError('Input data is not consistent with what point type requires: '
                                          + _FIELD_TYPE_MAPPING[typeid_list[0]][0])
 
-            else: # record array
+                # byteorder intepreting
+                if (data.dtype.byteorder == '<' and self.ptr().is_bigendian) or\
+                   (data.dtype.byteorder == '>' and not self.ptr().is_bigendian):
+                    ndtype = data.dtype
+                    ndtype.byteorder = '>' if self.ptr().is_bigendian else '<'
+                    data = data.astype(ndtype)
+
+            else: # [record array]
                 # data shape interpreting
                 if len(data.shape) < 1 or len(data.shape) > 2:
                     raise ValueError("Unrecognized input data shape")
@@ -171,11 +185,23 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
                     self.ptr().is_dense = True
 
                 # data field interpreting
-                self._ptype = _check_dtype_compatible(data.dtype)
-                if self._ptype.empty():
-                    raise ValueError("Inconsistent input numpy array dtype!")
+                if self._ptype.empty(): # not previously defined
+                    self._ptype = _check_dtype_compatible(data.dtype)
+                    if self._ptype.empty():
+                        raise ValueError("Inconsistent input numpy array dtype!")
                 self.ptr().point_step = data.strides[-1]
 
+                # byteorder intepreting
+                ndtype = {'names':[], 'formats':[]}
+                for subname in data.dtype.names:
+                    subtype = data.dtype[subname]
+                    if (subtype.byteorder == '<' and self.ptr().is_bigendian) or\
+                       (subtype.byteorder == '>' and not self.ptr().is_bigendian):
+                        subtype.byetorder = '>' if self.ptr().is_bigendian else '<'
+                    ndtype['names'].append(subname)
+                    ndtype['formats'].append(subtype)
+                data = data.astype(ndtype)
+
             # data strides calculation
             self.ptr().point_step = 0
             for name, typeid, count in _POINT_TYPE_MAPPING[self._ptype]:
@@ -189,14 +215,10 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
             self.ptr().row_step = self.ptr().point_step * self.ptr().width
 
             if not _is_not_record_array(data):
-                assert self.ptr().point_step != data.strides[-1]
+                assert self.ptr().point_step - data.strides[-1] == 0
 
             # data interpreting
-            # FIXME: generate warning if byte order is not consistent
-            if self.ptr().is_bigendian:
-                self.ptr().data = data.view('>u1').reshape(-1)
-            else:
-                self.ptr().data = data.view('<u1').reshape(-1)
+            self.ptr().data = data.view('B').ravel()
 
             initialized = True
         if data is None:
@@ -216,6 +238,10 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
         '''The fields of the point cloud'''
         def __get__(self): 
             return [PointField.wrap(field) for field in self.ptr().fields]
+    property names:
+        '''The name of the point cloud fields'''
+        def __get__(self): 
+            return [field.name.decode('ascii') for field in self.ptr().fields]
     property sensor_orientation:
         ''' Sensor acquisition pose (rotation). '''
         def __get__(self):
@@ -261,27 +287,42 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
         def __get__(self):
             cdef np.dtype struct = np.dtype([('b', 'u1'), ('g', 'u1'), ('r', 'u1'), ('a', 'u1')])
             return self.to_ndarray()['rgba'].view(struct)
+    property is_organized:
+        '''
+        Get whether the point cloud is organized
+        '''
 
     def __len__(self):
         return self.ptr().width * self.ptr().height
-
     def __repr__(self):
         return "<PointCloud of %d points>" % len(self)
-
-    def __iter__(self):
+    def __reduce__(self):
         raise NotImplementedError()
-
+    def __iter__(self):
+        return iter(self.to_ndarray())
     def __contains__(self, item):
-        raise NotImplementedError()
+        # for the field names, use 'names' property for instead.
+        return item in self.to_ndarray()
 
-    def __reduce__(self):
+    def __getitem__(self, indices):
+        raise NotImplementedError()
+    def __setitem__(self, indices, value):
+        raise NotImplementedError()
+    def __delitem__(self, indices):
         raise NotImplementedError()
 
     def __add__(self, item):
         raise NotImplementedError()
+    def __eq__(self, target):
+        raise NotImplementedError()
+
     def __array__(self, *_):
         '''support conversion to ndarray'''
         return self.to_ndarray()
+    def __getbuffer__(self, Py_buffer *buffer, int flags):
+        raise NotImplementedError()
+    def __releasebuffer__(self, Py_buffer *buffer):
+        raise NotImplementedError()
 
     cdef PCLPointCloud2* ptr(self):
         return self._ptr.get()
@@ -290,7 +331,7 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
         cdef uint8_t[:] mem_view = <uint8_t[:self.ptr().data.size()]>mem_ptr
         cdef np.ndarray arr_raw = np.asarray(mem_view)
         cdef str byte_order = '>' if self.ptr().is_bigendian else '<'
-        cdef list dtype = [(field.name, str(field.count) + byte_order + field.datatype)
+        cdef list dtype = [(field.name, str(field.count) + byte_order + field.npdtype)
                            for field in self.fields]
         cdef np.ndarray arr_view = arr_raw.view(dtype)
         return arr_view
@@ -308,34 +349,3 @@ cdef public class PointCloud[object CyPointCloud, type CyPointCloud_py]:
         Disorganize the point cloud. The function can act as updating function
         '''
         raise NotImplementedError()
-
-cdef str _nonzero_error_msg = "Function {0} returned {1}, please check stderr output!"
-
-# TODO: Inference point type from fields
-cpdef PointCloud load_pcd(str path):
-    cdef PointCloud cloud = PointCloud()
-    cdef int retval = loadPCDFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation)
-    if retval != 0: raise RuntimeError(_nonzero_error_msg.format("loadPCDFile", retval))
-    return cloud
-
-cpdef void save_pcd(str path, PointCloud cloud, PyBool binary=False):
-    cdef int retval = savePCDFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation, binary)
-    if retval != 0: raise RuntimeError(_nonzero_error_msg.format("savePCDFile", retval))
-
-# TODO: Inference point type from fields
-def load_ply(str path, type return_type=PointCloud):
-    cdef:
-        PointCloud cloud
-        int retval
-
-    if return_type == PointCloud:
-        cloud = PointCloud()
-        retval = loadPLYFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation)
-        if retval != 0: raise RuntimeError(_nonzero_error_msg.format("loadPLYFile", retval))
-        return cloud
-    else:
-        raise TypeError("Unsupported return type!")
-
-cpdef void save_ply(str path, PointCloud cloud, PyBool binary=False, PyBool use_camera=True):
-    cdef int retval = savePLYFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation, binary, use_camera)
-    if retval != 0: raise RuntimeError(_nonzero_error_msg.format("savePLYFile", retval))

pcl/PointField.pyx

@@ -22,18 +22,25 @@ cdef class PointField:
 
     property name:
         def __get__(self): return self.base.name.decode('ascii')
+        # def __set__(self, str value): self.base.name = value.encode('ascii')
 
     property count:
         def __get__(self): return self.base.count
+        # def __set__(self, int value): self.base.count = value
 
     property offset:
         def __get__(self): return self.base.offset
+        # def __set__(self, int value): self.base.offset = value
 
     property datatype:
+        def __get__(self): return self.base.datatype
+        # def __set__(self, unsigned char value): self.base.datatype = value
+
+    property npdtype:
         def __get__(self): return _FIELD_TYPE_MAPPING[self.base.datatype][0]
 
     def __repr__(self):
-        return "<PointField {0} : {1}>".format(self.name, self.datatype)
+        return "<PointField {0} : {1}>".format(self.name, self.npdtype)
 
     def to_msg(self):
         if not ros_exist: raise ros_error

pcl/__init__.py

@@ -1,3 +1,5 @@
 from .PointField import *
 from .PointCloud import *
 from .Visualizer import *
+
+from .io import *

pcl/io/CMakeLists.txt

@@ -0,0 +1,5 @@
+add_cython_target(_io CXX)
+add_library(_io MODULE ${_io})
+target_link_libraries(_io ${PCL_LIBRARIES})
+python_extension_module(_io)
+install(TARGETS _io LIBRARY DESTINATION pcl/io)

pcl/io/__init__.py

@@ -0,0 +1 @@
+from ._io import *

pcl/io/_io.pyx

@@ -0,0 +1,37 @@
+from cython.operator cimport dereference as deref
+from libcpp cimport bool
+
+from pcl.PointCloud cimport PointCloud
+from pcl.io.pcd_io cimport loadPCDFile, savePCDFile
+from pcl.io.ply_io cimport loadPLYFile, savePLYFile
+
+cdef str _nonzero_error_msg = "Function {0} returned {1}, please check stderr output!"
+
+# TODO: Inference point type from fields
+cpdef PointCloud load_pcd(str path):
+    cdef PointCloud cloud = PointCloud()
+    cdef int retval = loadPCDFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation)
+    if retval != 0: raise RuntimeError(_nonzero_error_msg.format("loadPCDFile", retval))
+    return cloud
+
+cpdef void save_pcd(str path, PointCloud cloud, bool binary=False):
+    cdef int retval = savePCDFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation, binary)
+    if retval != 0: raise RuntimeError(_nonzero_error_msg.format("savePCDFile", retval))
+
+# TODO: Inference point type from fields
+def load_ply(str path, type return_type=PointCloud):
+    cdef:
+        PointCloud cloud
+        int retval
+
+    if return_type == PointCloud:
+        cloud = PointCloud()
+        retval = loadPLYFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation)
+        if retval != 0: raise RuntimeError(_nonzero_error_msg.format("loadPLYFile", retval))
+        return cloud
+    else:
+        raise TypeError("Unsupported return type!")
+
+cpdef void save_ply(str path, PointCloud cloud, bool binary=False, bool use_camera=True):
+    cdef int retval = savePLYFile(path.encode('ascii'), deref(cloud._ptr), cloud._origin, cloud._orientation, binary, use_camera)
+    if retval != 0: raise RuntimeError(_nonzero_error_msg.format("savePLYFile", retval))

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name="PyPCL",
-    version="0.0.1",
+    version="0.1.1",
     description="Minial PCL Binding",
     author='Jacob Zhong',
     license="MIT",