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scripts/tap_const.py

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+from pathlib import Path
+
+import cv2
+
+parent = Path(__file__).parent.resolve()
+root = parent.joinpath("..").joinpath("..").resolve()
+
+datain = root.joinpath("datain").resolve()
+images = datain.joinpath("images").resolve()
+phenopsis = images.joinpath("phenopsis").resolve()
+cvpp = images.joinpath("Plant_Phenotyping_Datasets").resolve()
+param_set = images.joinpath("param_setting").resolve()
+param_set_images = images.joinpath("param_setting").joinpath("images").resolve()
+param_set_masks = images.joinpath("param_setting").joinpath("masks").resolve()
+param_set_thresholds = images.joinpath("param_setting").joinpath("thresholds").resolve()
+param_set_demo = images.joinpath("param_setting").joinpath("demo").resolve()
+param_set_gt_seg = (
+    images.joinpath("param_setting").joinpath("ground_truth_segmented").resolve()
+)
+param_set_train_data = images.joinpath("param_setting").joinpath("train_data").resolve()
+exp_phenopsis = datain.joinpath("phenopsis").resolve()
+data = datain.joinpath("data").resolve()
+datasets = datain.joinpath("datasets").resolve()
+
+dataout = root.joinpath("dataout").resolve()
+configurations = dataout.joinpath("confs").resolve()
+mask_cache = dataout.joinpath("masks").resolve()
+masks_raw = dataout.joinpath("raw_masks").resolve()
+
+checkpoints = root.joinpath("checkpoints").resolve()
+
+notebooks = root.joinpath("notebooks")
+scripts = notebooks.joinpath("scripts")
+
+# MARK: Constants
+DI_SRC = "source"
+DI_SRC_BBOXES = "Source with bboxes"
+
+DI_NONE = "no image"
+DI_SEG_SEED_MASK = "segmentation seed mask"
+DI_SEG_SEED_MASK_KEEP = "segmentation seed mask keep"
+DI_SEG_SEED_MASK_DISCARD = "segmentation seed mask discard"
+DI_SEG_DISTANCE_MAP = "segmentation distance map"
+DI_SEG_DISTANCE_MAP_KEEP = "segmentation distance map keep"
+DI_SEG_DISTANCE_MAP_DISCARD = "segmentation distance map discard"
+DI_SEG_DISTANCE_MAP_KEEP_WITH_SEEDS = "segmentation distance map keep with seeds"
+DI_SEG_DISTANCE_MAP_DISCARD_WITH_SEEDS = "segmentation distance map discard with seeds"
+DI_SEG_SEEDS = "segmentation seeds"
+DI_SEG_RAW_MASK = "segmentation raw mask"
+DI_SEG_LOW_RES_LOGITS_MASK = "segmentation low resolution logits mask"
+DI_SEG_EVOLVING_MASK = "segmentation mask progression"
+DI_SEG_CLEAN_MASK = "segmentation clean mask"
+DI_SEG_CLEAN_MASK_DEMO = "segmentation clean mask demo"
+DI_SEG_CLEAN_MASK_ON_IMAGE = "segmentation clean mask on image"
+DI_SEG_CONTOURS_ON_SRC_IMAGE = "contours on source image"
+DI_SEG_CLEAN_MASK_ON_IMAGE_WITH_CONTOURS = "clean mask on image with contours"
+DI_SEG_MASK_ON_IMAGE_SUSPECT_CONTOURS = "masked image with suspect contours"
+DI_SEG_CLEAN_MASK_ON_IMAGE_WTH_BOXES = "masked image with boxes"
+DI_SEG_CLEAN_MASK_ON_IMAGE_WITH_SEEDS = "segmentation clean mask on image with seeds"
+DI_SEG_PLANT_ONLY = "segmentation plant only"
+
+DI_SEQ_SRC_IMAGE = "source image"
+DI_SEG_RM_MASK = "raw mask"
+DI_SEQ_RM_PLANT = "plant only"
+DI_SEQ_RM_PLANT_HIGHLIGHT = "plant highlight"
+DF_SEQ_RM_CONTOURS = "plant with contours"
+DI_SEQ_RM_CONTOURS_HIERARCHY = "plant with contour hierarchy"
+DI_SEQ_RM_SUSPECT_CONTOURS = "plant and suspect contours"
+DI_SEQ_SM_MASK = "sifted mask"
+DI_SEQ_SM_PLANT = "sifted plant"
+DI_SEQ_SM_CONTOURS = "sifted plant with contours"
+DI_SEQ_SM_CONTOURS_ON_SRC = "source image with sifted contours"
+
+DI_SYMP_SEED_MASK = "symptoms seed mask"
+DI_SYMP_SEED_MASK_KEEP = "symptoms seed mask keep"
+DI_SYMP_SEED_MASK_DISCARD = "symptoms seed mask discard"
+DI_SYMP_SEEDS = "symptoms seeds"
+
+
+C_BLACK = (0, 0, 0)
+C_BLUE = (255, 0, 0)
+C_BLUE_VIOLET = (226, 43, 138)
+C_CABIN_BLUE = (209, 133, 67)
+C_CYAN = (255, 255, 0)
+C_DIM_GRAY = (105, 105, 105)
+C_FUCHSIA = (255, 0, 255)
+C_GREEN = (0, 128, 0)
+C_LIGHT_STEEL_BLUE = (222, 196, 176)
+C_LIME = (0, 255, 0)
+C_MAROON = (0, 0, 128)
+C_ORANGE = (80, 127, 255)
+C_PURPLE = (128, 0, 128)
+C_RED = (0, 0, 255)
+C_SILVER = (192, 192, 192)
+C_TEAL = (128, 128, 0)
+C_WHITE = (255, 255, 255)
+C_YELLOW = (0, 255, 255)
+C_BROWN = (42, 42, 165)
+C_SIENNA = (45, 82, 160)
+
+
+KLC_FULLY_INSIDE = dict(val=0, color=C_GREEN)
+KLC_OVERLAPS = dict(val=1, color=C_LIME)
+KLC_OK_TOLERANCE = dict(val=4, color=C_TEAL)
+KLC_SMALL = dict(val=5, color=C_BLUE)
+KLC_FAR = dict(val=6, color=C_RED)
+KLC_SMALL_FAR = dict(val=7, color=C_FUCHSIA)
+
+
+MP_HULL = "masp_property_hull"
+MP_CENTROID = "masp_property_centroid"
+MP_BOUND_RECT = "masp_property_bounding_rectangle"
+MP_ROT_BOUND_RECT = "masp_property_rotated_bounding_rectangle"
+MP_ENCLOSING_CIRCLE = "masp_property_enclosing_circle"
+AVAILABLE_MASK_PROPERTIES = [
+    MP_HULL,
+    MP_CENTROID,
+    MP_BOUND_RECT,
+    MP_ROT_BOUND_RECT,
+    MP_ENCLOSING_CIRCLE,
+]
+
+colors_dict = dict(
+    black=C_BLACK,
+    blue=C_BLUE,
+    blue_violet=C_BLUE_VIOLET,
+    blue_cabin=C_CABIN_BLUE,
+    cyan=C_CYAN,
+    dim_grey=C_DIM_GRAY,
+    fuchsia=C_FUCHSIA,
+    green=C_GREEN,
+    light_steel_blue=C_LIGHT_STEEL_BLUE,
+    lime=C_LIME,
+    maroon=C_MAROON,
+    orange=C_ORANGE,
+    purple=C_PURPLE,
+    red=C_RED,
+    silver=C_SILVER,
+    teal=C_TEAL,
+    white=C_WHITE,
+    yellow=C_YELLOW,
+    brown=C_BROWN,
+    sienna=C_SIENNA,
+)
+
+COLORS = [v for v in colors_dict.values()]
+
+channel_names = ["red", "green", "blue", "hue", "sat", "light"]
+channel_colors = {
+    "red": "red",
+    "green": "green",
+    "blue": "blue",
+    "hue": "orange",
+    "sat": "pink",
+    "light": "grey",
+}
+
+image_names = {
+    DI_NONE: "noImage",
+    DI_SEG_SEED_MASK: "segmentationSeedMask",
+    DI_SEG_SEED_MASK_KEEP: "segmentationMeedMaskKeep",
+    DI_SEG_SEED_MASK_DISCARD: "segmentationSeedMaskDiscard",
+    DI_SEG_DISTANCE_MAP: "segmentationDistanceMap",
+    DI_SEG_DISTANCE_MAP_KEEP: "segmentationDistanceMapKeep",
+    DI_SEG_DISTANCE_MAP_DISCARD: "segmentationDistanceMapDiscard",
+    DI_SEG_DISTANCE_MAP_KEEP_WITH_SEEDS: "segmentationDistanceMapKeepWithSeeds",
+    DI_SEG_DISTANCE_MAP_DISCARD_WITH_SEEDS: "segmentationDistanceMapDiscardWithSeeds",
+    DI_SEG_SEEDS: "segmentationSeeds",
+    DI_SEG_RAW_MASK: "segmentationRawMask",
+    DI_SEG_LOW_RES_LOGITS_MASK: "segmentationLowResolutionLogitsMask",
+    DI_SEG_EVOLVING_MASK: "segmentationMaskProgression",
+    DI_SEG_CLEAN_MASK: "segmentationCleanMask",
+    DI_SEG_CLEAN_MASK_DEMO: "segmentationCleanMaskDemo",
+    DI_SEG_CLEAN_MASK_ON_IMAGE: "segmentationCleanMaskOnImage",
+    DI_SEG_CLEAN_MASK_ON_IMAGE_WITH_CONTOURS: "cleanMaskOnImageWithContours",
+    DI_SEG_MASK_ON_IMAGE_SUSPECT_CONTOURS: "maskedImage",
+    DI_SEG_CLEAN_MASK_ON_IMAGE_WTH_BOXES: "maskedImageWith boxes",
+    DI_SEG_CLEAN_MASK_ON_IMAGE_WITH_SEEDS: "segmentationCleanMaskOnImageWithSeeds",
+    DI_SEG_PLANT_ONLY: "segmentationPlantOnly",
+    DI_SEQ_SRC_IMAGE: "sourceImage",
+    DI_SEG_RM_MASK: "rawMask",
+    DI_SEQ_RM_PLANT: "plantOnly",
+    DI_SEQ_RM_PLANT_HIGHLIGHT: "plantHighlight",
+    DF_SEQ_RM_CONTOURS: "plantWithContours",
+    DI_SEQ_RM_CONTOURS_HIERARCHY: "plantWithContourHierarchy",
+    DI_SEQ_RM_SUSPECT_CONTOURS: "plantAndSuspectContours",
+    DI_SEQ_SM_MASK: "siftedMask",
+    DI_SEQ_SM_PLANT: "siftedPlant",
+    DI_SEQ_SM_CONTOURS: "siftedPlantWithContours",
+    DI_SEQ_SM_CONTOURS_ON_SRC: "sourceImageWithSiftedContours",
+    DI_SYMP_SEED_MASK: "symptomsSeedMask",
+    DI_SYMP_SEED_MASK_KEEP: "symptomsSeedMaskKeep",
+    DI_SYMP_SEED_MASK_DISCARD: "symptomsSeedMaskDiscard",
+    DI_SYMP_SEEDS: "symptomsSeeds",
+}
+
+
+OPENCV_DIST_METHODS = {
+    "Correlation": cv2.HISTCMP_CORREL,
+    "Chi-Squared": cv2.HISTCMP_CHISQR,
+    "Intersection": cv2.HISTCMP_INTERSECT,
+    "Hellinger": cv2.HISTCMP_BHATTACHARYYA,
+}
+
+THS_SOURCE = "source"
+THS_RAW_MASK_PLANT = "raw plant mask"
+THS_MASK_PLANT = "plant mask"
+THS_RAW_MASK_BACKGROUND = "raw background mask"
+THS_MASK_BACKGROUND = "background mask"
+THS_MASK_PLANT_REGIONS = "plant mask regions"
+THS_MASK_BACKGROUND_REGIONS = "background mask regions"
+THS_MASK_MERGED = "merged mask"
+THS_MASK_REGIONS = "regions"
+THS_MASK_SEEDS = "merged mask with seeds"
+THS_MASK_REGIONS_SEEDS = "regions with seeds"
+THS_SEG_MASK_RAW = "raw mask"
+THS_SEG_MASK_CLEAN = "clean mask"
+THS_SEG_MASK_DEMO = "demo klc mask"
+THS_SEG_MASK_LOGITS = "logits"
+THS_SEG_MASK_EVO = "segmentation evolution"
+THS_SEG_PLANT_ONLY = "plant only"
+THS_SEG_PLANT_DEMO = "plant demo"
+
+AVAILABLE_IMAGES = [
+    THS_SOURCE,
+    THS_RAW_MASK_PLANT,
+    THS_MASK_PLANT,
+    THS_RAW_MASK_BACKGROUND,
+    THS_MASK_BACKGROUND,
+    THS_MASK_MERGED,
+    THS_MASK_REGIONS,
+    THS_MASK_REGIONS_SEEDS,
+    THS_MASK_SEEDS,
+    THS_SEG_MASK_RAW,
+    THS_SEG_MASK_CLEAN,
+    THS_SEG_MASK_DEMO,
+    THS_SEG_MASK_LOGITS,
+    THS_SEG_MASK_EVO,
+    THS_SEG_PLANT_ONLY,
+    THS_SEG_PLANT_DEMO,
+]