From c0cde8d585d574ffc2dde59d8887d284e9997002 Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <maciej.wielgosz@nibio.no>
Date: Tue, 8 Nov 2022 14:50:50 +0100
Subject: [PATCH] first version for the sweep test pipeline
---
pipeline_test.py | 111 +++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 111 insertions(+)
create mode 100644 pipeline_test.py
diff --git a/pipeline_test.py b/pipeline_test.py
new file mode 100644
index 0000000..f5875a0
--- /dev/null
+++ b/pipeline_test.py
@@ -0,0 +1,111 @@
+import subprocess
+import wandb
+
+# local imports
+from metrics.instance_segmentation_metrics_in_folder import InstanceSegmentationMetricsInFolder
+
+# wandb.login()
+
+# wandb.init(project="instance_segmentation_classic", entity="smart_forest")
+
+# define a class to run the command with arguments
+class RunCommand:
+ def __init__(self, cmd, args):
+ self.cmd = cmd
+ self.args = args
+
+ def __call__(self):
+ print("Running command: " + self.cmd + " " + " ".join(self.args))
+ subprocess.run([self.cmd, *self.args])
+
+# define the sweep configuration with the parameters to sweep
+sweep_configuration = {
+ 'method': 'random',
+ 'name': 'sweep',
+ 'metric': {'goal': 'maximize', 'name': 'f1_score'},
+ 'parameters':
+ {
+ 'N_TILES': {'values': [3]},
+ 'SLICE_THICKNESS': {'values': [0.5]},
+ 'FIND_STEMS_HEIGHT': {'values': [1.5]},
+ 'FIND_STEMS_THICKNESS': {'values': [0.5]},
+ 'GRAPH_MAXIMUM_CUMULATIVE_GAP': {'values': [3]},
+ 'ADD_LEAVES_VOXEL_LENGTH': {'values': [0.5]},
+ 'FIND_STEMS_MIN_POINTS': {'values': [50, 100, 150]}
+ }
+}
+
+def main():
+ # initialize the sweep
+ run = wandb.init(project="sweep-train", entity="maciej-wielgosz-nibio")
+ # get files for the sweep
+ print("Getting files for the sweep")
+ cmd = "/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/bash_helper_scripts/get_small_data_for_playground.sh"
+ subprocess.run([cmd], shell=True)
+
+ # define the arguments for all the parameters from the sweep configuration
+ print("Defining arguments for all the parameters from the sweep configuration")
+ n_tiles = wandb.config.N_TILES
+ slice_thickness = wandb.config.SLICE_THICKNESS
+ find_stems_height = wandb.config.FIND_STEMS_HEIGHT
+ find_stems_thickness = wandb.config.FIND_STEMS_THICKNESS
+ graph_maximum_cumulative_gap = wandb.config.GRAPH_MAXIMUM_CUMULATIVE_GAP
+ add_leaves_voxel_length = wandb.config.ADD_LEAVES_VOXEL_LENGTH
+ find_stems_min_points = wandb.config.FIND_STEMS_MIN_POINTS
+
+ # print the arguments
+ print("N_TILES: " + str(n_tiles))
+ print("SLICE_THICKNESS: " + str(slice_thickness))
+ print("FIND_STEMS_HEIGHT: " + str(find_stems_height))
+ print("FIND_STEMS_THICKNESS: " + str(find_stems_thickness))
+ print("GRAPH_MAXIMUM_CUMULATIVE_GAP: " + str(graph_maximum_cumulative_gap))
+ print("ADD_LEAVES_VOXEL_LENGTH: " + str(add_leaves_voxel_length))
+ print("FIND_STEMS_MIN_POINTS: " + str(find_stems_min_points))
+
+
+ # define the command
+ cmd = "./run_all_command_line.sh"
+
+ # define the arguments
+ args = [
+ "-d", "/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground"
+ ]
+
+ print("Adding the arguments to the list of arguments")
+ args.extend([
+ "-n", str(n_tiles),
+ "-s", str(slice_thickness),
+ "-h", str(find_stems_height),
+ "-t", str(find_stems_thickness),
+ "-g", str(graph_maximum_cumulative_gap),
+ "-l", str(add_leaves_voxel_length),
+ "-m", str(find_stems_min_points)
+ ])
+
+ # run the command with the arguments
+ print("Running the command with the arguments")
+ RunCommand(cmd, args)()
+
+ # compute the metric
+ print("Computing the metric")
+ metric = InstanceSegmentationMetricsInFolder(
+ gt_las_folder_path = '/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/input_data',
+ target_las_folder_path = '/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds_with_ground',
+ gt_label_name='treeID',
+ target_label_name='treeID',
+ verbose=True
+ )
+
+ f1_score = metric.main()
+ print("F1 score: " + str(f1_score))
+
+ # log the metric
+ print("Logging the metric")
+ wandb.log({"f1_score": f1_score})
+
+
+# define the sweep
+sweep_id = wandb.sweep(sweep=sweep_configuration, project="sweep-train", entity="maciej-wielgosz-nibio")
+
+# run the sweep
+wandb.agent(sweep_id, function=main, count=2)
\ No newline at end of file
--
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