Update scanline functions and get_pr/lr_pts function in series class. #32

linwang9926 · 2023-06-09T23:35:55Z

Update scanline functions
Update get_pr/lr_pts function in series class.
Update stem width function
Disable warning spam from nan/empty slice operations (Disable warning spam from nan/empty slice operations #34 ).

codecov · 2023-06-09T23:42:09Z

Codecov Report

Merging #32 (2abac65) into main (e8b9eed) will increase coverage by 15.21%.
The diff coverage is 90.69%.

@@             Coverage Diff             @@
##             main      #32       +/-   ##
===========================================
+ Coverage   67.37%   82.59%   +15.21%     
===========================================
  Files          13       13               
  Lines         656      678       +22     
===========================================
+ Hits          442      560      +118     
+ Misses        214      118       -96

Impacted Files	Coverage Δ
sleap_roots/traitsgraph.py	`100.00% <ø> (ø)`
sleap_roots/bases.py	`97.82% <66.66%> (+5.43%)`	⬆️
sleap_roots/networklength.py	`92.53% <71.42%> (-2.71%)`	⬇️
sleap_roots/points.py	`97.05% <75.00%> (-2.95%)`	⬇️
sleap_roots/series.py	`39.58% <80.00%> (+2.81%)`	⬆️
sleap_roots/graphpipeline.py	`95.38% <93.97%> (+80.13%)`	⬆️
sleap_roots/scanline.py	`97.36% <95.45%> (+2.13%)`	⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

talmo

mostly minor changes, except one special case that may lead to errors

talmo · 2023-06-21T03:36:44Z

sleap_roots/graphpipeline.py

+            type(fn_outputs) == np.float64
+            or type(fn_outputs) == float
+            or type(fn_outputs) == np.int64
+            or type(fn_outputs) == int


Suggested change

type(fn_outputs) == np.float64

or type(fn_outputs) == float

or type(fn_outputs) == np.int64

or type(fn_outputs) == int

isinstance(fn_outputs, (np.floating, float))

or isinstance(fn_outputs, (np.integer, int))

talmo · 2023-06-21T03:37:25Z

sleap_roots/graphpipeline.py

+        gt_instances_pr = primary.user_instances + primary.unused_predictions
+        gt_instances_lr = lateral.user_instances + lateral.unused_predictions
+
+        # lateral_pts = lateral.numpy()


remove unused comment

talmo · 2023-06-21T03:38:57Z

sleap_roots/graphpipeline.py

    for i in range(len(SCALAR_TRAITS)):
        if SCALAR_TRAITS[i] in column_names:
-            trait = data_plant[SCALAR_TRAITS[i]].values
+            trait = data_plant_df[SCALAR_TRAITS[i]]
+            # LW start


remove unused comment

talmo · 2023-06-21T03:40:33Z

sleap_roots/graphpipeline.py

+                    type(trait[0]) == int
+                    or type(trait[0]) == np.int64
+                    or type(trait[0]) == np.float64
+                    or type(trait[0]) == float


Suggested change

type(trait[0]) == int

or type(trait[0]) == np.int64

or type(trait[0]) == np.float64

or type(trait[0]) == float

isinstance(trait[0], (np.floating, float))

or isinstance(trait[0], (np.integer, int))

talmo · 2023-06-21T03:42:35Z

sleap_roots/graphpipeline.py

+                    or type(trait[0]) == np.float64
+                    or type(trait[0]) == float
+                ):
+                    values = np.array([element[0] for element in trait])


Won't this break if trait contains scalars? Like if type(trait[0]) == int, then for example:

trait = [0, 1, 2] assert type(trait[0]) == int element = trait[0] element[0] # error

I remembered that the trait is like: [[0,1,2]].
The test of the pipeline is good, but I met a problem using Spyder to run code with new environment, will fix it soon

I will modify it together with issue #33

talmo · 2023-06-21T03:44:36Z

sleap_roots/scanline.py

-        intersection_line = []
-        for j in range(len(points)):
+    for i in range(n_line):  # n_line
+        # y_loc = n_interval * (i + 1)


remove unused comment

talmo · 2023-06-21T03:44:41Z

sleap_roots/scanline.py

+    for i in range(n_line):  # n_line
+        # y_loc = n_interval * (i + 1)
+        horizontal_line_y = n_interval * (i + 1)
+        # line = LineString([(0, y_loc), (width, y_loc)])


remove unused comment

talmo · 2023-06-21T03:44:50Z

sleap_roots/scanline.py

            # filter out nan nodes
            pts_j = np.array(points[j])[~np.isnan(points[j]).any(axis=1)]
+            # print(pts_j)


remove unused comment

talmo · 2023-06-21T03:45:03Z

sleap_roots/scanline.py

+                        y1 < horizontal_line_y and y2 >= horizontal_line_y
+                    ):
+                        current_root += 1
+                        # is_inside_root = not is_inside_root


remove unused comment

talmo · 2023-06-21T03:45:10Z

sleap_roots/scanline.py

+                        current_root += 1
+                        # is_inside_root = not is_inside_root
+                intersection_counts_root += current_root
+                # print(intersection_counts_root)


remove unused comment

…into lin/pipeline_graph_plant_quick

…#32) * Update scanline functions and get_pr/lr_pts function in series class. * fix case where points are in a list * Specified SLEAP version * Uncomment graphpipeline tests * Bump version requirement for sleap-io * Use isinstance and remove commented lines. * Black format of graphpipeline.py and scanline.py. * Disable warning spam from nan/empty slice operations. --------- Co-authored-by: Lin Wang <linwang9926@gmail.com> Co-authored-by: Elizabeth Berrigan <berri104@gmail.com> Co-authored-by: Talmo Pereira <talmo@salk.edu>

Update scanline functions and get_pr/lr_pts function in series class.

0c75043

linwang9926 requested a review from talmo June 13, 2023 17:10

talmo requested changes Jun 21, 2023

View reviewed changes

eberrigan and others added 10 commits June 21, 2023 21:44

fix case where points are in a list

11056ad

Specified SLEAP version

46200ca

Merge branch 'main' into lin/pipeline_graph_plant_quick

1f9f1e1

Uncomment graphpipeline tests

19f8c67

Bump version requirement for sleap-io

2f66f0d

Merge branch 'main' into lin/pipeline_graph_plant_quick

4ac3125

Merge remote-tracking branch 'origin/lin/pipeline_graph_plant_quick' …

2160b65

…into lin/pipeline_graph_plant_quick

Use isinstance and remove commented lines.

65d1063

Black format of graphpipeline.py and scanline.py.

f11bdd7

Disable warning spam from nan/empty slice operations.

2abac65

linwang9926 mentioned this pull request Jun 26, 2023

Disable warning spam from nan/empty slice operations #34

Closed

talmo approved these changes Jun 26, 2023

View reviewed changes

linwang9926 merged commit db93e0d into main Jun 26, 2023

talmo deleted the lin/pipeline_graph_plant_quick branch July 5, 2023 16:37

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Update scanline functions and get_pr/lr_pts function in series class. #32

Update scanline functions and get_pr/lr_pts function in series class. #32

linwang9926 commented Jun 9, 2023 •

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codecov bot commented Jun 9, 2023 •

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talmo Jun 21, 2023

Update scanline functions and get_pr/lr_pts function in series class. #32

Update scanline functions and get_pr/lr_pts function in series class. #32

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linwang9926 commented Jun 9, 2023 • edited Loading

codecov bot commented Jun 9, 2023 • edited Loading

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linwang9926 commented Jun 9, 2023 •

edited

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codecov bot commented Jun 9, 2023 •

edited

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