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globals.py
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globals.py
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from PyQt5.QtGui import QIcon, QColor
from typings import Workflow, WorkflowObj
from typing import List
""" VERSION NUMBER """
VERSION_NUMBER: str = '1.3.0'
"""
WORKFLOW METADATA
___________________
Array of JSON objects containing the following data:
@name:
@type: ENUM type of Workflow
@header: string displayed as "header"
@desc: string displayed as "description" below header
@checked: is workflow checked by default
@graph: graph metadata:
@type: type of graph
@title: title of graph
@x_label: x_label of graph
@y_label: y_label of graph
@x_type: the value measured on x axis
@y_type: the value measured on y axis
@props: array of optional parameters in the following format:
@title: title of prop
@placeholder: placeholder for prop label
"""
# TODO: ADD NEW WORKFLOW METADATA HERE
WORKFLOWS: List[WorkflowObj] = [
{
"name": "NND",
"type": Workflow.NND,
"header": "Nearest Neighbor Distance of Particles",
"desc": "Find the nearest neighbor distance (NND) between gold particles. Optionally generate random coordinates.",
"checked": True,
"graph": {
"type": "hist",
"title": "NND of Particles",
"x_label": "Distance",
"y_label": "Number of Particles",
"x_type": "dist"
},
"props": []
},
{
"name": "CLUST",
"type": Workflow.CLUST,
"header": "Hierarchical Clustering of Particles",
"desc": "Cluster gold particles into groups. Optionally generate random coordinates.",
"checked": True,
"graph": {
"type": "bar",
"title": "Hierarchical Clustering of Particles",
"x_label": "Number of Particles In Cluster",
"y_label": "Number of Clusters",
"x_type": "cluster_id",
"y_type": "cluster_id"
},
"props": [
{
"title": "distance threshold (px)",
"placeholder": "27"
}
]
},
{
"name": "SEPARATION",
"type": Workflow.SEPARATION,
"header": "Separation Between Clusters",
"desc": "Find the separation (NND) between clusters. Optionally generate random coordinates.",
"checked": True,
"graph": {
"type": "hist",
"title": "Separation Between Clusters",
"x_label": "Nearest Neighbor Distance",
"y_label": "Number of Entries",
"x_type": "dist",
},
"props": [
{
"title": "distance threshold (px)",
"placeholder": "27"
},
{
"title": "minimum clust size",
"placeholder": "2"
},
]
},
{
"name": "RIPPLER",
"type": Workflow.RIPPLER,
"header": "Gold Rippler: Landmark-Particle Correlation",
"desc": "Separate landmark masks as individual components, grow components until they contain X gold particles, calculate Landmark Correlated Particle Index (LCPI): (% of gold particles within landmark masks) / (% of total area of img taken up by landmark masks). Requires lighthouse population.",
"checked": False,
"graph": {
"type": "bar",
"title": "Landmark Correlated Particle Index (LCPI) By Radius",
"x_label": "radius",
"y_label": "LCPI",
"x_type": "radius",
"y_type": "LCPI"
},
"props": [
{
"title": "maximum steps",
"placeholder": "10"
},
{
"title": "step size (px)",
"placeholder": "60"
},
{
"title": "initial radius (px)",
"placeholder": "50"
}
]
},
{
"name": "GOLDSTAR",
"type": Workflow.GOLDSTAR,
"header": "Gold Star Nearest Neighbor Distance",
"desc": "Find the nearest neighbor distance of two different populations. Requires lighthouse population",
"checked": False,
"graph": {
"type": "hist",
"title": "Gold Star NND",
"x_label": "Distance",
"y_label": "Number of Particles",
"x_type": "dist"
},
"props": [
{
"title": "A* (around landmarks)",
"placeholder": "0"
}
]
},
{
"name": "ASTAR",
"type": Workflow.ASTAR,
"header": "A* NND Around Landmarks",
"desc": "Find the nearest neighbor distance of two different populations around landmarks. Requires lighthouse population",
"checked": False,
"graph": {
"type": "hist",
"title": "A* NND",
"x_label": "Distance",
"y_label": "Number of Particles",
"x_type": "dist"
},
"props": []
},
]
""" COLOR PALETTE OPTIONS """
PALETTE_OPS: List[str] = ["rocket", "crest", "mako", "flare", "viridis", "magma", "cubehelix", "rocket_r", "mako_r", "crest_r",
"flare_r", "viridis_r", "magma_r", ]
REAL_COLOR = (212, 118, 41)
RAND_COLOR = (62, 193, 213)
""" METRIC UNIT OPTIONS """
UNIT_OPS: List[str] = ['px', 'nm', 'μm', 'metric']
""" UNIT SCALARS """
UNIT_PX_SCALARS = {
'px': 1,
'nm': 0.888, # 1 px = 0.888nm
'μm': 0.000888, # 1px = 0.000888μm
'metric': 1
}
""" NAVBAR ICON """
NAV_ICON = QIcon('foo.png')
""" MAX DIRS TO KEEP WHEN PRUNING OLD DIRS """
MAX_DIRS_PRUNE: int = 5
""" DEFAULT OUTPUT DIRECTORY """
DEFAULT_OUTPUT_DIR: str = './output'
""" RANDOM COORDINATES DEFAULT DISTANCE THRESHOLD (px) """
DEFAULT_DISTANCE_THRESH = 5
""" PROGRESS BAR COLORS """
PROG_COLOR_1 = QColor(221, 221, 221)
PROG_COLOR_2 = QColor(0, 190, 204)