Coverage for src/cell_abm_pipeline/flows/sample_image.py: 0%

1""" 

2Workflow for sampling cell ids from an image. 

3 

4Working location structure: 

5 

6.. code-block:: bash 

7 

8 (name) 

9 ├── images 

10 │ └── (name)_(key).(extension) 

11 ├── plots 

12 │ └── plots.SAMPLE 

13 │ └── (name)_(key)_C(channel)_R(resolution).SAMPLE.png 

14 └── samples 

15 └── samples.RAW 

16 └── (name)_(key)_C(channel)_R(resolution).RAW.csv 

17 

18Input images to be sampled are loaded from **images**. Resulting image sample(s) 

19are placed into **samples.RAW** and corresponding contact sheet(s) are placed 

20into **plots.SAMPLE**. 

21""" 

22 

23from dataclasses import dataclass, field 

24from typing import Optional 

25 

26from abm_initialization_collection.image import get_image_bounds, plot_contact_sheet 

27from abm_initialization_collection.sample import ( 

28 get_image_samples, 

29 get_sample_indices, 

30 scale_sample_coordinates, 

31) 

32from io_collection.keys import make_key 

33from io_collection.load import load_image 

34from io_collection.save import save_dataframe, save_figure 

35from prefect import flow 

36 

37# Default pixel resolution for images in x/y in um/pixel 

38SCALE_MICRONS_XY: float = 0.108333 

39 

40# Default pixel resolution for images in z in um/pixel 

41SCALE_MICRONS_Z: float = 0.29 

42 

43 

44@dataclass 

45class ParametersConfig: 

46 """Parameter configuration for sample image flow.""" 

47 

48 key: str 

49 """Image key to sample.""" 

50 

51 channels: list[int] = field(default_factory=lambda: [0]) 

52 """Image channels to sample.""" 

53 

54 grid: str = "rect" 

55 """Type of sampling grid (rect = rectangular, hex = hexagonal).""" 

56 

57 coordinate_type: Optional[str] = None 

58 """Coordinate scaling type (None = unscaled, absolute = in um, step = by step size).""" 

59 

60 resolution: float = 1.0 

61 """Distance between samples in um.""" 

62 

63 scale_xy: float = SCALE_MICRONS_XY 

64 """ Resolution scaling in x/y in um/pixel.""" 

65 

66 scale_z: float = SCALE_MICRONS_Z 

67 """Resolution scaling in z in um/pixel.""" 

68 

69 extension: str = ".ome.tiff" 

70 """Image extension.""" 

71 

72 contact_sheet: bool = True 

73 """True to save contact sheet of processed samples, False otherwise.""" 

74 

75 

76@dataclass 

77class ContextConfig: 

78 """Context configuration for sample image flow.""" 

79 

80 working_location: str 

81 """Location for input and output files (local path or S3 bucket).""" 

82 

83 

84@dataclass 

85class SeriesConfig: 

86 """Series configuration for sample image flow.""" 

87 

88 name: str 

89 """Name of the simulation series.""" 

90 

91 

92@flow(name="sample-image") 

93def run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) -> None: 

94 """Main sample image flow.""" 

95 

96 image_key = make_key( 

97 series.name, "images", f"{series.name}_{parameters.key}{parameters.extension}" 

98 ) 

99 image = load_image( 

100 context.working_location, 

101 image_key, 

102 dim_order="ZYX" if parameters.extension == ".tiff" else None, 

103 ) 

104 image_bounds = get_image_bounds(image) 

105 

106 sample_indices = get_sample_indices( 

107 parameters.grid, 

108 image_bounds, 

109 parameters.resolution, 

110 parameters.scale_xy, 

111 parameters.scale_z, 

112 ) 

113 

114 for channel in parameters.channels: 

115 resolution_key = f"R{round(parameters.resolution * 10):03d}" 

116 channel_key = f"C{channel:02d}" 

117 item_key = f"{series.name}_{parameters.key}_{channel_key}_{resolution_key}" 

118 

119 samples = get_image_samples(image, sample_indices, channel) 

120 samples = scale_sample_coordinates( 

121 samples, 

122 parameters.coordinate_type, 

123 parameters.resolution, 

124 parameters.scale_xy, 

125 parameters.scale_z, 

126 ) 

127 sample_key = make_key(series.name, "samples", "samples.RAW", f"{item_key}.RAW.csv") 

128 save_dataframe(context.working_location, sample_key, samples, index=False) 

129 

130 if parameters.contact_sheet: 

131 contact_sheet = plot_contact_sheet(samples) 

132 plot_key = make_key(series.name, "plots", "plots.SAMPLE", f"{item_key}.SAMPLE.png") 

133 save_figure(context.working_location, plot_key, contact_sheet)