def write_default_header(self):
imf = self.image_file
imf.extensionsAdd("", libe57.E57_V1_0_URI)
self.root.set("formatName", libe57.StringNode(imf, "ASTM E57 3D Imaging Data File"))
self.root.set("guid", libe57.StringNode(imf, "{%s}" % uuid.uuid4()))
self.root.set("versionMajor", libe57.IntegerNode(imf, libe57.E57_FORMAT_MAJOR))
self.root.set("versionMinor", libe57.IntegerNode(imf, libe57.E57_FORMAT_MINOR))
self.root.set("e57LibraryVersion", libe57.StringNode(imf, libe57.E57_LIBRARY_ID))
self.root.set("coordinateMetadata", libe57.StringNode(imf, ""))
creation_date_time = libe57.StructureNode(imf)
creation_date_time.set("dateTimeValue", libe57.FloatNode(imf, 0.0))
creation_date_time.set("isAtomicClockReferenced", libe57.IntegerNode(imf, 0))
self.root.set("creationDateTime", creation_date_time)
self.root.set("data3D", libe57.VectorNode(imf, True))
self.root.set("images2D", libe57.VectorNode(imf, True))
def write_scan_raw(self,
data: Dict,
*,
name=None,
rotation=None,
translation=None,
scan_header=None):
for field in data.keys():
if field not in SUPPORTED_POINT_FIELDS:
raise ValueError("Unsupported point field: %s" % field)
if rotation is None:
rotation = getattr(scan_header, "rotation", np.array([1, 0, 0, 0]))
if translation is None:
translation = getattr(scan_header, "translation",
np.array([0, 0, 0]))
if name is None:
name = getattr(scan_header, "name", "Scan %s" % len(self.data3d))
temperature = getattr(scan_header, "temperature", 0)
relativeHumidity = getattr(scan_header, "relativeHumidity", 0)
atmosphericPressure = getattr(scan_header, "atmosphericPressure", 0)
scan_node = libe57.StructureNode(self.image_file)
scan_node.set(
"guid", libe57.StringNode(self.image_file, "{%s}" % uuid.uuid4()))
scan_node.set("name", libe57.StringNode(self.image_file, name))
scan_node.set("temperature",
libe57.FloatNode(self.image_file, temperature))
scan_node.set("relativeHumidity",
libe57.FloatNode(self.image_file, relativeHumidity))
scan_node.set("atmosphericPressure",
libe57.FloatNode(self.image_file, atmosphericPressure))
scan_node.set(
"description",
libe57.StringNode(self.image_file, "pye57 v%s" % __version__))
n_points = data["cartesianX"].shape[0]
ibox = libe57.StructureNode(self.image_file)
if "rowIndex" in data and "columnIndex" in data:
min_row = np.min(data["rowIndex"])
max_row = np.max(data["rowIndex"])
min_col = np.min(data["columnIndex"])
max_col = np.max(data["columnIndex"])
ibox.set("rowMinimum", libe57.IntegerNode(self.image_file,
min_row))
ibox.set("rowMaximum", libe57.IntegerNode(self.image_file,
max_row))
ibox.set("columnMinimum",
libe57.IntegerNode(self.image_file, min_col))
ibox.set("columnMaximum",
libe57.IntegerNode(self.image_file, max_col))
else:
ibox.set("rowMinimum", libe57.IntegerNode(self.image_file, 0))
ibox.set("rowMaximum",
libe57.IntegerNode(self.image_file, n_points - 1))
ibox.set("columnMinimum", libe57.IntegerNode(self.image_file, 0))
ibox.set("columnMaximum", libe57.IntegerNode(self.image_file, 0))
ibox.set("returnMinimum", libe57.IntegerNode(self.image_file, 0))
ibox.set("returnMaximum", libe57.IntegerNode(self.image_file, 0))
scan_node.set("indexBounds", ibox)
if "intensity" in data:
int_min = getattr(scan_header, "intensityMinimum",
np.min(data["intensity"]))
int_max = getattr(scan_header, "intensityMaximum",
np.max(data["intensity"]))
intbox = libe57.StructureNode(self.image_file)
intbox.set("intensityMinimum",
libe57.FloatNode(self.image_file, int_min))
intbox.set("intensityMaximum",
libe57.FloatNode(self.image_file, int_max))
scan_node.set("intensityLimits", intbox)
color = all(c in data for c in ["colorRed", "colorGreen", "colorBlue"])
if color:
colorbox = libe57.StructureNode(self.image_file)
colorbox.set("colorRedMinimum",
libe57.IntegerNode(self.image_file, 0))
colorbox.set("colorRedMaximum",
libe57.IntegerNode(self.image_file, 255))
colorbox.set("colorGreenMinimum",
libe57.IntegerNode(self.image_file, 0))
colorbox.set("colorGreenMaximum",
libe57.IntegerNode(self.image_file, 255))
colorbox.set("colorBlueMinimum",
libe57.IntegerNode(self.image_file, 0))
colorbox.set("colorBlueMaximum",
libe57.IntegerNode(self.image_file, 255))
scan_node.set("colorLimits", colorbox)
bbox_node = libe57.StructureNode(self.image_file)
x, y, z = data["cartesianX"], data["cartesianY"], data["cartesianZ"]
valid = None
if "cartesianInvalidState" in data:
valid = ~data["cartesianInvalidState"].astype("?")
x, y, z = x[valid], y[valid], z[valid]
bb_min = np.array([x.min(), y.min(), z.min()])
bb_max = np.array([x.max(), y.max(), z.max()])
del valid, x, y, z
if scan_header is not None:
bb_min_scaled = np.array([
scan_header.xMinimum, scan_header.yMinimum,
scan_header.zMinimum
])
bb_max_scaled = np.array([
scan_header.xMaximum, scan_header.yMaximum,
scan_header.zMaximum
])
else:
bb_min_scaled = self.to_global(bb_min.reshape(-1, 3), rotation,
translation)[0]
bb_max_scaled = self.to_global(bb_max.reshape(-1, 3), rotation,
translation)[0]
bbox_node.set("xMinimum",
libe57.FloatNode(self.image_file, bb_min_scaled[0]))
bbox_node.set("xMaximum",
libe57.FloatNode(self.image_file, bb_max_scaled[0]))
bbox_node.set("yMinimum",
libe57.FloatNode(self.image_file, bb_min_scaled[1]))
bbox_node.set("yMaximum",
libe57.FloatNode(self.image_file, bb_max_scaled[1]))
bbox_node.set("zMinimum",
libe57.FloatNode(self.image_file, bb_min_scaled[2]))
bbox_node.set("zMaximum",
libe57.FloatNode(self.image_file, bb_max_scaled[2]))
scan_node.set("cartesianBounds", bbox_node)
if rotation is not None and translation is not None:
pose_node = libe57.StructureNode(self.image_file)
scan_node.set("pose", pose_node)
rotation_node = libe57.StructureNode(self.image_file)
rotation_node.set("w",
libe57.FloatNode(self.image_file, rotation[0]))
rotation_node.set("x",
libe57.FloatNode(self.image_file, rotation[1]))
rotation_node.set("y",
libe57.FloatNode(self.image_file, rotation[2]))
rotation_node.set("z",
libe57.FloatNode(self.image_file, rotation[3]))
pose_node.set("rotation", rotation_node)
translation_node = libe57.StructureNode(self.image_file)
translation_node.set(
"x", libe57.FloatNode(self.image_file, translation[0]))
translation_node.set(
"y", libe57.FloatNode(self.image_file, translation[1]))
translation_node.set(
"z", libe57.FloatNode(self.image_file, translation[2]))
pose_node.set("translation", translation_node)
start_datetime = getattr(scan_header, "acquisitionStart_dateTimeValue",
0)
start_atomic = getattr(scan_header,
"acquisitionStart_isAtomicClockReferenced",
False)
end_datetime = getattr(scan_header, "acquisitionEnd_dateTimeValue", 0)
end_atomic = getattr(scan_header,
"acquisitionEnd_isAtomicClockReferenced", False)
acquisition_start = libe57.StructureNode(self.image_file)
scan_node.set("acquisitionStart", acquisition_start)
acquisition_start.set(
"dateTimeValue", libe57.FloatNode(self.image_file, start_datetime))
acquisition_start.set(
"isAtomicClockReferenced",
libe57.IntegerNode(self.image_file, start_atomic))
acquisition_end = libe57.StructureNode(self.image_file)
scan_node.set("acquisitionEnd", acquisition_end)
acquisition_end.set("dateTimeValue",
libe57.FloatNode(self.image_file, end_datetime))
acquisition_end.set("isAtomicClockReferenced",
libe57.IntegerNode(self.image_file, end_atomic))
# todo: pointGroupingSchemes
points_prototype = libe57.StructureNode(self.image_file)
is_scaled = False
precision = libe57.E57_DOUBLE if is_scaled else libe57.E57_SINGLE
center = (bb_max + bb_min) / 2
chunk_size = 5000000
x_node = libe57.FloatNode(self.image_file, center[0], precision,
bb_min[0], bb_max[0])
y_node = libe57.FloatNode(self.image_file, center[1], precision,
bb_min[1], bb_max[1])
z_node = libe57.FloatNode(self.image_file, center[2], precision,
bb_min[2], bb_max[2])
points_prototype.set("cartesianX", x_node)
points_prototype.set("cartesianY", y_node)
points_prototype.set("cartesianZ", z_node)
field_names = ["cartesianX", "cartesianY", "cartesianZ"]
if "intensity" in data:
intensity_min = np.min(data["intensity"])
intensity_max = np.max(data["intensity"])
intensity_node = libe57.FloatNode(self.image_file, intensity_min,
precision, intensity_min,
intensity_max)
points_prototype.set("intensity", intensity_node)
field_names.append("intensity")
if all(color in data
for color in ["colorRed", "colorGreen", "colorBlue"]):
points_prototype.set(
"colorRed", libe57.IntegerNode(self.image_file, 0, 0, 255))
points_prototype.set(
"colorGreen", libe57.IntegerNode(self.image_file, 0, 0, 255))
points_prototype.set(
"colorBlue", libe57.IntegerNode(self.image_file, 0, 0, 255))
field_names.append("colorRed")
field_names.append("colorGreen")
field_names.append("colorBlue")
if "rowIndex" in data and "columnIndex" in data:
min_row = np.min(data["rowIndex"])
max_row = np.max(data["rowIndex"])
min_col = np.min(data["columnIndex"])
max_col = np.max(data["columnIndex"])
points_prototype.set(
"rowIndex",
libe57.IntegerNode(self.image_file, 0, min_row, max_row))
field_names.append("rowIndex")
points_prototype.set(
"columnIndex",
libe57.IntegerNode(self.image_file, 0, min_col, max_col))
field_names.append("columnIndex")
if "cartesianInvalidState" in data:
min_state = np.min(data["cartesianInvalidState"])
max_state = np.max(data["cartesianInvalidState"])
points_prototype.set(
"cartesianInvalidState",
libe57.IntegerNode(self.image_file, 0, min_state, max_state))
field_names.append("cartesianInvalidState")
# other fields
# // "sphericalRange"
# // "sphericalAzimuth"
# // "sphericalElevation"
# // "timeStamp"
# // "sphericalInvalidState"
# // "isColorInvalid"
# // "isIntensityInvalid"
# // "isTimeStampInvalid"
arrays, buffers = self.make_buffers(field_names, chunk_size)
codecs = libe57.VectorNode(self.image_file, True)
points = libe57.CompressedVectorNode(self.image_file, points_prototype,
codecs)
scan_node.set("points", points)
self.data3d.append(scan_node)
writer = points.writer(buffers)
current_index = 0
while current_index != n_points:
current_chunk = min(n_points - current_index, chunk_size)
for type_ in SUPPORTED_POINT_FIELDS:
if type_ in arrays:
arrays[type_][:current_chunk] = data[type_][
current_index:current_index + current_chunk]
writer.write(current_chunk)
current_index += current_chunk
writer.close()