Merge pull request #232 from JoQCcoz/adding_offset

Added stage limits

Smartscope/core/db_manipulations.py

@@ -131,7 +131,8 @@ def group_holes_for_BIS(hole_models, max_radius=4, min_group_size=1, queue_all=F
         f'grouping params, max radius = {max_radius}, min group size = {min_group_size}, queue all = {queue_all}, max iterations = {iterations}, score_weight = {score_weight}')
     # Extract coordinated for the holes
     prefetch_related_objects(hole_models, 'finders')
-    coords = np.array([[list(h.finders.all())[0].stage_x, list(h.finders.all())[0].stage_y] for h in hole_models])
+    coords = []
+    coords = np.array([h.stage_coords for h in hole_models])
     input_number = len(hole_models)
     # Generate distance matrix
     cd = cdist(coords, coords)
@@ -282,7 +283,7 @@ def add_high_mag(grid, parent):
 
 def select_n_squares(parent, n):
     squares = np.array(parent.squaremodel_set.all().filter(selected=False, status=None).order_by('area'))
-    squares = [s for s in squares if s.is_good()]
+    squares = [s for s in squares if s.is_good() and not s.is_out_of_range()]
     if len(squares) == 0:
         return
     split_squares = np.array_split(squares, n)
@@ -302,7 +303,7 @@ def select_n_holes(parent, n, is_bis=False):
     holes = list(parent.holemodel_set.filter(
         **filter_fields).order_by('dist_from_center'))
 
-    holes = [h for h in holes if h.is_good()]
+    holes = [h for h in holes if h.is_good() and not h.is_out_of_range()]
 
     if n <= 0:
         with transaction.atomic():
@@ -340,13 +341,13 @@ def select_n_areas(parent, n, is_bis=False):
     if n <= 0:
         with transaction.atomic():
             for t in targets:
-                if t.is_good() and not t.is_excluded()[0]:
+                if t.is_good() and not t.is_excluded()[0] and not t.is_out_of_range():
                     update(t, selected=True, status='queued')
         return
 
     clusters = dict()
     for t in targets:
-        if not t.is_good():
+        if not t.is_good() or t.is_out_of_range():
             continue
         excluded, label = t.is_excluded()
         if excluded:

Smartscope/core/grid/run_square.py

@@ -54,7 +54,7 @@ def process_square_image(square, grid, microscope_id):
             if is_bis:
                 holes = list(HoleModel.display.filter(square_id=square.square_id))
                 holes = group_holes_for_BIS(
-                    [h for h in holes if h.is_good() and not h.is_excluded()[0]],
+                    [h for h in holes if h.is_good() and not h.is_excluded()[0] and not h.is_out_of_range()],
                     max_radius=grid.params_id.bis_max_distance,
                     min_group_size=grid.params_id.min_bis_group_size
                 )

Smartscope/core/main_commands.py

@@ -122,13 +122,8 @@ def regroup_bis(grid_id, square_id):
     holes_for_grouping = []
     other_holes = []
     for h in filtered_holes:
-
-        # h.bis_group = None
-        # h.bis_type = None
-        if h.is_good() and not h.is_excluded()[0]:
+        if h.is_good() and not h.is_excluded()[0] and not h.is_out_of_range():
             holes_for_grouping.append(h)
-        # else:
-        #     other_holes.append(h)
 
     logger.info(f'Filtered holes = {len(filtered_holes)}\nHoles for grouping = {len(holes_for_grouping)}')
 

Smartscope/core/models/target.py

@@ -82,6 +82,8 @@ def is_good(self):
                 return False
         return True
 
+    def is_out_of_range(self) -> bool:
+        return not self.finders.first().is_position_within_stage_limits()
     # def css_color(self, display_type, method):
 
     #     if method is None:

Smartscope/core/models/target_label.py

@@ -3,6 +3,7 @@
 '''
 from django.contrib.contenttypes.fields import GenericForeignKey
 from django.contrib.contenttypes.models import ContentType
+import math
 
 from .base_model import *
 
@@ -32,6 +33,13 @@ class Finder(TargetLabel):
     class Meta(BaseModel.Meta):
         db_table = 'finder'
 
+    def radius_from_origin(self, offset_x=0, offset_y=0) -> float:
+        return math.sqrt((self.stage_x + offset_x) ** 2 + (self.stage_y + offset_y) ** 2)
+
+    def is_position_within_stage_limits(self, stage_radius_limit:int = 975, offset_x:float=0, offset_y:float=0) -> bool:
+        ##NEED TO ADD OFFSETS AND NOT HARDCODE THE LIMIT
+        return self.radius_from_origin(offset_x=offset_x,offset_y=offset_y) <= stage_radius_limit
+
 
 class Classifier(TargetLabel):
     label = models.CharField(max_length=30, null=True)

Smartscope/core/svg_plots.py

@@ -91,6 +91,9 @@ def drawAtlas(atlas, targets, display_type, method) -> draw.Drawing:
         if color is not None:
             sz = floor(sqrt(i.area))
             finder = list(i.finders.all())[0]
+            if not finder.is_position_within_stage_limits():
+                color = '#505050'
+                label = 'Out of range'
             x = finder.x - sz // 2
             y = (finder.y - sz // 2)
             r = draw.Rectangle(x, y, sz, sz, id=i.pk, stroke_width=floor(d.width / 300), stroke=color, fill=color, fill_opacity=0, label=label,
@@ -131,6 +134,9 @@ def drawSquare(square, targets, display_type, method) -> draw.Drawing:
         color, label, prefix = css_color(i, display_type, method)
         if color is not None:
             finder = list(i.finders.all())[0]
+            if not finder.is_position_within_stage_limits():
+                color = '#505050'
+                label = 'Out of range'
             x = finder.x
             y = finder.y
             c = draw.Circle(x, y, i.radius, id=i.pk, stroke_width=floor(d.width / 250), stroke=color, fill=color, fill_opacity=0, label=label,

static/reports.js

@@ -118,6 +118,9 @@ $('#main').on('click', '.showLegend', function () {
 
 
 function selectElement(elem, selection) {
+    if (elem.getAttribute('label') == 'Out of range') {
+        return
+    }
     if (selection.includes(elem.id)) {
         console.log('Unselecting')
         elem.classList.remove('clicked')