From 6e5b633edf229077bb088f2e38bbf01f9135a2ec Mon Sep 17 00:00:00 2001
From: swittl <simon.wittl@th-deg.de>
Date: Thu, 27 Jun 2024 14:33:26 +0200
Subject: [PATCH] added volume io
---
example/volume_example.py | 28 +++++
rq_controller.egg-info/PKG-INFO | 7 +-
rq_controller.egg-info/SOURCES.txt | 23 +++-
.../__pycache__/__init__.cpython-38.pyc | Bin 0 -> 153 bytes
rq_controller/common/__init__.py | 2 +-
.../__pycache__/projection.cpython-38.pyc | Bin 3604 -> 4308 bytes
.../region_of_intrest.cpython-38.pyc | Bin 1505 -> 2410 bytes
.../io/__pycache__/writer.cpython-38.pyc | Bin 2453 -> 3569 bytes
rq_controller/common/io/loader.py | 15 ++-
.../__pycache__/__init__.cpython-38.pyc | Bin 179 -> 264 bytes
.../__pycache__/json_load.cpython-38.pyc | Bin 0 -> 2445 bytes
.../__pycache__/json_write.cpython-38.pyc | Bin 0 -> 2611 bytes
rq_controller/common/io/rq_json/json_load.py | 30 ++++--
rq_controller/common/io/rq_json/json_write.py | 14 ++-
rq_controller/common/io/writer.py | 22 +++-
rq_controller/common/projection.py | 9 +-
rq_controller/common/region_of_intrest.py | 32 +++---
rq_controller/common/volume.py | 101 ++++++++++++++++++
rq_controller/rq_workflow.py | 1 +
19 files changed, 246 insertions(+), 38 deletions(-)
create mode 100644 example/volume_example.py
create mode 100644 rq_controller/__pycache__/__init__.cpython-38.pyc
create mode 100644 rq_controller/common/io/rq_json/__pycache__/json_load.cpython-38.pyc
create mode 100644 rq_controller/common/io/rq_json/__pycache__/json_write.cpython-38.pyc
create mode 100644 rq_controller/common/volume.py
diff --git a/example/volume_example.py b/example/volume_example.py
new file mode 100644
index 0000000..b0574ec
--- /dev/null
+++ b/example/volume_example.py
@@ -0,0 +1,28 @@
+from rq_controller.common import PyVolume
+from rq_controller.common.io.rq_json import RqJsonWriter, RqJsonLoader
+from pathlib import Path
+
+
+FOLDER = Path('./example/data')
+
+
+def main():
+ volume = PyVolume.dummy()
+ print(f'Shape (x / y / z): {volume.shape}')
+ msg = volume.as_message()
+ print(f'Number of slices: {len(msg.slices)}')
+
+ volume_2 = PyVolume.from_message(msg)
+ print(f'Shape (x / y / z): {volume_2.shape}')
+
+ writer = RqJsonWriter()
+ writer.write_volume(writer.get_volume_save_path_i(FOLDER, 1), volume_2)
+
+ loader = RqJsonLoader()
+ volume_3 = loader.load_volume(writer.get_volume_save_path_i(FOLDER, 1))
+ print(f'Shape (x / y / z): {volume_3.shape}')
+
+
+if __name__ == '__main__':
+ main()
+
diff --git a/rq_controller.egg-info/PKG-INFO b/rq_controller.egg-info/PKG-INFO
index fd6b18a..1fb26ba 100644
--- a/rq_controller.egg-info/PKG-INFO
+++ b/rq_controller.egg-info/PKG-INFO
@@ -1,8 +1,11 @@
Metadata-Version: 2.1
-Name: rq_controller
+Name: rq-controller
Version: 0.0.0
Summary: TODO: Package description
Maintainer: root
Maintainer-email: simon.wittl@th-deg.de
License: TODO: License declaration
-Requires-Dist: setuptools
+Platform: UNKNOWN
+
+UNKNOWN
+
diff --git a/rq_controller.egg-info/SOURCES.txt b/rq_controller.egg-info/SOURCES.txt
index 14660b4..19eb469 100644
--- a/rq_controller.egg-info/SOURCES.txt
+++ b/rq_controller.egg-info/SOURCES.txt
@@ -1,10 +1,16 @@
+.gitignore
README.md
package.xml
setup.cfg
setup.py
+.vscode/c_cpp_properties.json
+.vscode/settings.json
+example/projection_example.py
+example/data/projection_00001.geom-json
+example/data/projection_00001.tif
resource/rq_controller
rq_controller/__init__.py
-rq_controller/rq_workflow_client.py
+rq_controller/rq_workflow.py
rq_controller.egg-info/PKG-INFO
rq_controller.egg-info/SOURCES.txt
rq_controller.egg-info/dependency_links.txt
@@ -15,12 +21,23 @@ rq_controller/common/__init__.py
rq_controller/common/projection.py
rq_controller/common/projection_geometry.py
rq_controller/common/region_of_intrest.py
+rq_controller/common/volume.py
+rq_controller/common/__pycache__/__init__.cpython-38.pyc
+rq_controller/common/__pycache__/projection.cpython-38.pyc
+rq_controller/common/__pycache__/projection_geometry.cpython-38.pyc
+rq_controller/common/__pycache__/region_of_intrest.cpython-38.pyc
rq_controller/common/io/__init__.py
rq_controller/common/io/loader.py
rq_controller/common/io/writer.py
+rq_controller/common/io/__pycache__/__init__.cpython-38.pyc
+rq_controller/common/io/__pycache__/loader.cpython-38.pyc
+rq_controller/common/io/__pycache__/writer.cpython-38.pyc
rq_controller/common/io/rq_json/__init__.py
-rq_controller/common/io/rq_json/load.py
-rq_controller/common/io/rq_json/write.py
+rq_controller/common/io/rq_json/json_load.py
+rq_controller/common/io/rq_json/json_write.py
+rq_controller/common/io/rq_json/__pycache__/__init__.cpython-38.pyc
+rq_controller/common/io/rq_json/__pycache__/load.cpython-38.pyc
+rq_controller/common/io/rq_json/__pycache__/write.cpython-38.pyc
test/test_copyright.py
test/test_flake8.py
test/test_pep257.py
\ No newline at end of file
diff --git a/rq_controller/__pycache__/__init__.cpython-38.pyc b/rq_controller/__pycache__/__init__.cpython-38.pyc
new file mode 100644
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diff --git a/rq_controller/common/__init__.py b/rq_controller/common/__init__.py
index c737cfd..49190b8 100644
--- a/rq_controller/common/__init__.py
+++ b/rq_controller/common/__init__.py
@@ -1,2 +1,2 @@
from .projection import PyProjectionGeometry, PyProjection
-from .region_of_intrest import PyRegionOfIntrest
\ No newline at end of file
+from .volume import PyVolume, PyRegionOfIntrest
\ No newline at end of file
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diff --git a/rq_controller/common/io/loader.py b/rq_controller/common/io/loader.py
index fe8c5b0..4ce8e32 100644
--- a/rq_controller/common/io/loader.py
+++ b/rq_controller/common/io/loader.py
@@ -1,25 +1,30 @@
import numpy as np
import json
from pathlib import Path
-from ...common import PyProjectionGeometry, PyProjection, PyRegionOfIntrest
+from ...common import PyProjectionGeometry, PyProjection, PyRegionOfIntrest, PyVolume
class BaseDataLoader():
def __init__(self,
porjection_geometry_suffix: str,
projection_suffix: str,
- region_of_intrest_suffix: str):
+ region_of_intrest_suffix: str,
+ volume_suffix: str):
self.porjection_geometry_suffix = porjection_geometry_suffix
self.projection_suffix = projection_suffix
self.region_of_intrest_suffix = region_of_intrest_suffix
+ self.volume_suffix = volume_suffix
def load_projection_geometry(self, load_path: Path) -> PyProjectionGeometry:
- raise NotImplementedError
+ raise NotImplementedError()
def load_projection(self, load_path: Path) -> PyProjection:
- raise NotImplementedError
+ raise NotImplementedError()
def load_region_of_intrest(self, load_path: Path) -> PyRegionOfIntrest:
- raise NotImplementedError
+ raise NotImplementedError()
+
+ def load_volume(self, load_path: Path) -> PyVolume:
+ raise NotImplementedError()
\ No newline at end of file
diff --git a/rq_controller/common/io/rq_json/__pycache__/__init__.cpython-38.pyc b/rq_controller/common/io/rq_json/__pycache__/__init__.cpython-38.pyc
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diff --git a/rq_controller/common/io/rq_json/json_load.py b/rq_controller/common/io/rq_json/json_load.py
index 2727ef3..d414d60 100644
--- a/rq_controller/common/io/rq_json/json_load.py
+++ b/rq_controller/common/io/rq_json/json_load.py
@@ -2,13 +2,15 @@ import numpy as np
import json
from pathlib import Path
-from ..loader import BaseDataLoader, PyProjection, PyProjectionGeometry, PyRegionOfIntrest
+from ..loader import BaseDataLoader, PyProjection, PyProjectionGeometry, PyRegionOfIntrest, PyVolume
from PIL import Image
+import xtiff
+import pyometiff
class RqJsonLoader(BaseDataLoader):
def __init__(self):
- super().__init__('.geom-json', '.tif', '.roi-json')
+ super().__init__('.geom-json', '.tif', '.roi-json', '.ome.tiff')
def load_json(self, load_path: Path) -> dict:
with open(str(load_path), 'r') as f:
@@ -51,9 +53,25 @@ class RqJsonLoader(BaseDataLoader):
data_dict = self.load_json(load_path)
region_of_intrest = PyRegionOfIntrest(
- start_point_mm=np.array(data_dict['start_point_mm']),
- end_point_mm=np.array(data_dict['end_point_mm']),
- frame_id=data_dict['resoluion_mm'],
- resoluion_mm=np.array(data_dict['resoluion_mm']))
+ center_points_mm=np.array(data_dict['center_points_mm']),
+ dimensions_mm=np.array(data_dict['dimensions_mm']),
+ frame_id=data_dict['frame_id'],
+ resolution_mm=np.array(data_dict['resolution_mm']))
return region_of_intrest
+
+ def load_volume(self, load_path: Path) -> PyVolume:
+ load_path_roi = load_path.parent / f'{load_path.stem}{self.region_of_intrest_suffix}'
+ roi = self.load_region_of_intrest(load_path_roi)
+ reader = pyometiff.OMETIFFReader(load_path)
+ volume, _, _ = reader.read()
+
+ if volume.dtype == np.uint16:
+ data_type = 0
+ elif volume.dtype == np.uint8:
+ data_type = 1
+ else:
+ raise ValueError('data type not implemented.')
+
+ return PyVolume(volume, roi, data_type)
+
diff --git a/rq_controller/common/io/rq_json/json_write.py b/rq_controller/common/io/rq_json/json_write.py
index 4099fa9..2628163 100644
--- a/rq_controller/common/io/rq_json/json_write.py
+++ b/rq_controller/common/io/rq_json/json_write.py
@@ -2,13 +2,15 @@ import numpy as np
import json
from pathlib import Path
-from ..writer import BaseDataWriter, PyProjection, PyProjectionGeometry, PyRegionOfIntrest
+from ..writer import BaseDataWriter, PyProjection, PyProjectionGeometry, PyRegionOfIntrest, PyVolume
from PIL import Image
+import xtiff
+import pyometiff
class RqJsonWriter(BaseDataWriter):
def __init__(self):
- super().__init__('.geom-json', '.tif', '.roi-json')
+ super().__init__('.geom-json', '.tif', '.roi-json', '.ome.tiff')
def write_json(self, save_path: Path, data_dict: dict):
with open(str(save_path), 'w') as f:
@@ -61,6 +63,12 @@ class RqJsonWriter(BaseDataWriter):
data_dict['center_points_mm'] = region_of_intrest.center_points_mm.tolist()
data_dict['dimensions_mm'] = region_of_intrest.dimensions_mm.tolist()
data_dict['frame_id'] = region_of_intrest.frame_id
- data_dict['resoluion_mm'] = region_of_intrest.resolution_mm.tolist()
+ data_dict['resolution_mm'] = region_of_intrest.resolution_mm.tolist()
self.write_json(save_path, data_dict)
+
+ def write_volume(self, save_path: Path, volume: PyVolume):
+ save_path_region_of_intrest = save_path.parent / f'{save_path.stem}{self.region_of_intrest_suffix}'
+ self.write_region_of_intrest(save_path_region_of_intrest, volume.roi)
+ writer = pyometiff.OMETIFFWriter(save_path, volume.array, dict())
+ writer.write()
\ No newline at end of file
diff --git a/rq_controller/common/io/writer.py b/rq_controller/common/io/writer.py
index 73f1c40..be86283 100644
--- a/rq_controller/common/io/writer.py
+++ b/rq_controller/common/io/writer.py
@@ -1,31 +1,36 @@
import numpy as np
import json
from pathlib import Path
-from ...common import PyProjectionGeometry, PyProjection, PyRegionOfIntrest
+from ...common import PyProjectionGeometry, PyProjection, PyRegionOfIntrest, PyVolume
class BaseDataWriter():
projection_name: str = 'projection'
projection_geometry_name: str ='geometry'
region_of_intrest_name: str = 'roi'
+ volume_name: str = 'volume'
def __init__(self,
porjection_geometry_suffix: str,
projection_suffix: str,
- region_of_intrest_suffix: str):
+ region_of_intrest_suffix: str,
+ volume_suffix: str):
self.porjection_geometry_suffix = porjection_geometry_suffix
self.projection_suffix = projection_suffix
self.region_of_intrest_suffix = region_of_intrest_suffix
+ self.volume_suffix = volume_suffix
def write_projection_geometry(self, save_path: Path, projection_geometry: PyProjectionGeometry):
- raise NotImplementedError
+ raise NotImplementedError()
def write_projection(self, save_path: Path, projection: PyProjection):
- raise NotImplementedError
+ raise NotImplementedError()
def write_region_of_intrest(self, save_path: Path, region_of_intrest: PyRegionOfIntrest):
raise NotImplementedError
+ def write_volume(save_path: Path, region_of_intrest: PyRegionOfIntrest):
+ raise NotImplementedError()
def get_next_projection_save_path(self, save_folder: Path) -> Path:
return self.get_projection_save_path_i(save_folder, self.number_of_projections(save_folder) + 1)
@@ -45,6 +50,12 @@ class BaseDataWriter():
def get_region_of_intrest_save_path_i(self, save_folder: Path, i) -> Path:
return save_folder / f'{self.region_of_intrest_name}_{i:05}{self.region_of_intrest_suffix}'
+ def get_next_volume_save_path(self, save_folder: Path) -> Path:
+ return self.get_volume_save_path_i(save_folder, self.number_of_volumes(save_folder) + 1)
+
+ def get_volume_save_path_i(self, save_folder: Path, i) -> Path:
+ return save_folder / f'{self.volume_name}_{i:05}{self.volume_suffix}'
+
def number_of_projection_geometries(self, folder: Path) -> int:
return len(list(folder.glob(f'{self.projection_geometry_name}*{self.porjection_geometry_suffix}')))
@@ -53,3 +64,6 @@ class BaseDataWriter():
def number_of_region_of_intrests(self, folder: Path) -> int:
return len(list(folder.glob(f'{self.region_of_intrest_name}*{self.region_of_intrest_suffix}')))
+
+ def number_of_volumes(self, folder: Path) -> int:
+ return len(list(folder.glob(f'{self.volume_name}*{self.volume_suffix}')))
diff --git a/rq_controller/common/projection.py b/rq_controller/common/projection.py
index 979e8f4..ea5c1ee 100644
--- a/rq_controller/common/projection.py
+++ b/rq_controller/common/projection.py
@@ -114,6 +114,13 @@ class PyProjection(PyProjectionGeometry):
return message
+ def get_projection_geometry(self) -> PyProjectionGeometry:
+ return PyProjectionGeometry(self.focal_spot_mm,
+ self.detector_postion_mm,
+ self.detector_orientation_quad,
+ self.frame_id,
+ self.focal_spot_orientation_quad)
+
@property
def detector_heigth_px(self) -> int:
return self.image.shape[0]
@@ -128,4 +135,4 @@ class PyProjection(PyProjectionGeometry):
@property
def pixel_pitch_y_mm(self) -> float:
- return self.detector_heigth_mm / self.detector_heigth_px
\ No newline at end of file
+ return self.detector_heigth_mm / self.detector_heigth_px
diff --git a/rq_controller/common/region_of_intrest.py b/rq_controller/common/region_of_intrest.py
index 1636edd..6a3115b 100644
--- a/rq_controller/common/region_of_intrest.py
+++ b/rq_controller/common/region_of_intrest.py
@@ -7,15 +7,15 @@ from visualization_msgs.msg import Marker
class PyRegionOfIntrest():
def __init__(self, center_points_mm: np.ndarray, dimensions_mm: np.ndarray, frame_id: str = 'object',
resolution_mm: np.ndarray = np.array([0.1, 0.1, 0.1])):
- self.center_points_mm = center_points_mm
- self.dimensions_mm = dimensions_mm
+ self.center_points_mm = center_points_mm.reshape((-1, 3))
+ self.dimensions_mm = dimensions_mm.reshape((-1, 3))
self.frame_id = frame_id
- self.resolution_mm = resolution_mm
+ self.resolution_mm = resolution_mm.reshape((-1, 3))
@classmethod
def dummy(cls):
return cls((np.random.random((3, )) - 0.5) * 20.,
- (np.random.random((3, )) - 0.5) * 10.)
+ np.random.random((3, )) * 10.)
@classmethod
def from_message(cls, msg: RegionOfIntrest):
@@ -45,6 +45,12 @@ class PyRegionOfIntrest():
def number_of_rois(self) -> int:
return self.center_points_mm.shape[0]
+ @property
+ def shape(self) -> tuple:
+ shape = self.dimensions_mm[0] // self.resolution_mm[0]
+ return (int(shape[0]), int(shape[1]), int(shape[2]))
+
+
def as_message(self) -> RegionOfIntrest:
message = RegionOfIntrest()
roi_list = list()
@@ -52,13 +58,13 @@ class PyRegionOfIntrest():
for i in range(self.number_of_rois):
roi = Marker()
- roi.pose.position.x = self.center_points_mm[i][0]
- roi.pose.position.y = self.center_points_mm[i][1]
- roi.pose.position.z = self.center_points_mm[i][2]
+ roi.pose.position.x = float(self.center_points_mm[i][0])
+ roi.pose.position.y = float(self.center_points_mm[i][1])
+ roi.pose.position.z = float(self.center_points_mm[i][2])
- roi.scale.x = self.dimensions_mm[i][0]
- roi.scale.y = self.dimensions_mm[i][1]
- roi.scale.z = self.dimensions_mm[i][2]
+ roi.scale.x = float(self.dimensions_mm[i][0])
+ roi.scale.y = float(self.dimensions_mm[i][1])
+ roi.scale.z = float(self.dimensions_mm[i][2])
roi.header.frame_id = self.frame_id
@@ -66,8 +72,8 @@ class PyRegionOfIntrest():
message.region_of_intrest_stack.markers = roi_list
- message.resolution.x = self.resolution_mm[0]
- message.resolution.x = self.resolution_mm[1]
- message.resolution.x = self.resolution_mm[2]
+ message.resolution.x = float(self.resolution_mm[0][0])
+ message.resolution.y = float(self.resolution_mm[0][1])
+ message.resolution.z = float(self.resolution_mm[0][2])
return message
diff --git a/rq_controller/common/volume.py b/rq_controller/common/volume.py
new file mode 100644
index 0000000..3ac025e
--- /dev/null
+++ b/rq_controller/common/volume.py
@@ -0,0 +1,101 @@
+from numpy import ndarray
+from numpy.core.multiarray import array as array
+from rq_interfaces.msg import Volume
+from visualization_msgs.msg import Marker
+from .region_of_intrest import PyRegionOfIntrest
+from sensor_msgs.msg import Image
+from enum import IntEnum
+
+import numpy as np
+import ros2_numpy
+
+
+class VOLUME_TYPES(IntEnum):
+ UINT_16 = 0
+ UINT_8 = 1
+
+
+class PyVolume():
+ def __init__(self, array: ndarray, roi: PyRegionOfIntrest, data_type: VOLUME_TYPES = ...):
+ self.roi = roi
+ self.array = array
+ self.data_typ = data_type
+
+ @staticmethod
+ def get_data_type(volume_type: VOLUME_TYPES) -> np.dtype:
+ if volume_type == VOLUME_TYPES.UINT_16:
+ return np.uint16
+ elif volume_type == VOLUME_TYPES.UINT_8:
+ return np.uint8
+ else:
+ raise ValueError('Datatype is not implemented')
+
+ @staticmethod
+ def enum_to_numpify(volume_type: VOLUME_TYPES) -> str:
+ if volume_type == VOLUME_TYPES.UINT_16:
+ return 'mono16'
+ elif volume_type == VOLUME_TYPES.UINT_8:
+ return 'mono8'
+ else:
+ raise ValueError('Datatype is not implemented')
+
+ @classmethod
+ def dummy(cls):
+ roi = PyRegionOfIntrest.dummy()
+ array = np.random.randint(0, 255, size=roi.shape)
+ data_type = VOLUME_TYPES.UINT_8
+ return cls(array, roi, data_type)
+
+ @classmethod
+ def from_message(cls, msg: Volume):
+ roi: Marker = msg.grid.region_of_intrest_stack.markers[0]
+ center_points_mm = np.array([
+ roi.pose.position.x,
+ roi.pose.position.y,
+ roi.pose.position.z])
+
+ dimensions_mm = np.array([
+ roi.scale.x,
+ roi.scale.y,
+ roi.scale.z])
+
+ frame_id = roi.header.frame_id
+ resolution_mm = np.array([
+ msg.grid.resolution.x,
+ msg.grid.resolution.y,
+ msg.grid.resolution.z])
+
+ py_roi = PyRegionOfIntrest(center_points_mm, dimensions_mm, frame_id, resolution_mm)
+
+ data_typ = msg.datatype
+
+ array = np.zeros(py_roi.shape, dtype=cls.get_data_type(data_typ))
+
+ for i, slice in enumerate(msg.slices):
+ array[:, :, i] = ros2_numpy.numpify(slice).reshape((py_roi.shape[0], py_roi.shape[1])).astype(cls.get_data_type(data_typ))
+
+ return cls(array, py_roi, data_typ)
+
+ def as_message(self) -> Volume:
+ message = Volume()
+
+ message.datatype = self.data_typ
+ message.grid = self.roi.as_message()
+ message.slices = list()
+
+ for z in range(self.array.shape[2]):
+ message.slices.append(
+ ros2_numpy.msgify(Image,
+ self.array[:, :, z].astype(self.get_data_type(self.data_typ)),
+ self.enum_to_numpify(self.data_typ)))
+
+ return message
+
+ @property
+ def shape(self):
+ return self.array.shape
+
+
+
+
+
diff --git a/rq_controller/rq_workflow.py b/rq_controller/rq_workflow.py
index 662b0c7..b729565 100644
--- a/rq_controller/rq_workflow.py
+++ b/rq_controller/rq_workflow.py
@@ -51,6 +51,7 @@ class WorkflowNode(Node):
reached, cost, _ = self.hardware_interface.reachability_response_2_py(response)
return reached, cost
+
def main():
rclpy.init()
--
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