Merge pull request #33 from New-Horizons-SPM/CI-server2

CI-Server2
New-Horizons-SPM · Mar 23, 2024 · 54dd645 · 54dd645
2 parents 984acf1 + b6181aa
commit 54dd645
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diff --git a/.github/workflows/windows-install.yml b/.github/workflows/windows-install.yml
@@ -20,11 +20,6 @@ jobs:
 
     - name: Setup Node.js
       uses: actions/setup-node@v4
-
-    - name: Install dependent repository
-      run: |
-        cd nanonisTCP
-        pip install .
 
     - name: Install node_modules and build the app
       env:

diff --git a/scanbot/server/server.py b/scanbot/server/server.py
@@ -167,7 +167,7 @@ def run_go_to_target():
 @app.route('/scanbot_config')
 def get_config():
     sbConfig = scanbot_config(module_dir=app.module_dir)
-    return {'config': sbConfig.config}
+    return {'config': sbConfig.config}, 200
 
 @app.route('/save_config', methods=['POST'])
 def save_config():

diff --git a/scanbot/server/test_server.py b/scanbot/server/test_server.py
@@ -6,6 +6,9 @@
 import time
 import cv2
 import os
+from PIL import Image
+import base64
+import io
 
 @pytest.fixture
 def client(tmp_path):
@@ -14,11 +17,17 @@ def client(tmp_path):
         yield client
 
 def test_homepage(client):
+    """
+    Test that the server is able to provide the homepage
+    """
     response = client.get('/')
     homepage_found = response.data.decode().startswith('<!doctype html>')
     assert homepage_found == True
 
 def test_has_config(client, tmp_path):
+    """
+    Test that the config file can be found
+    """
     fake_file = tmp_path / "scanbot_config.ini"
     fake_file.write_text("test")
 
@@ -29,29 +38,50 @@ def test_has_config(client, tmp_path):
     assert file_found == True
 
 def test_has_no_config(client):
+    """
+    Test that the config file can't be found
+    """
     response = client.get('/has_config')
     json_data = response.json
     file_found = json_data['status']
 
     assert file_found == False
 
 def test_test_connection(client):
-    response = client.get('/test_connection')
-    assert response.status_code == 200          # Hard to test anything else here since nanonis needs to be open
+    """
+    Test that the connection to nanonis can be verified
+    """
+    with patch('scanbot.server.scanbot.nanonisTCP') as mock_nanonisTCP, \
+         patch('scanbot.server.scanbot.Bias') as mock_Bias:
+
+        mock_nanonisTCP.return_value.close_connection.return_value = None
+
+        mock_Bias.return_value.Get.return_value = 0 # Scanbot tests the connection by attempting to read the bias value in nanonis. Give it something
+
+        response = client.get('/test_connection')
+        assert response.status_code == 200
+
+        json_data = response.json
+        connected = json_data['status']
+        assert connected
 
 def test_reset_init(client):
+    """
+    Test that the tip initiliasation can be reset
+    """
     response = client.get('/reset_init')
     json_data = response.json
     success = json_data['status']
 
     assert response.status_code == 200
     assert success == "success"
 
-# %%
-# Test demo initialisation
-# 
-# First test that /is_auto_init returns False (since initialisation has not been run yet)
+# Test initialisation
+
 def test_is_not_auto_init(client):
+    """
+    Test to see if initialisation is not complete
+    """
     response     = client.get('/is_auto_init')
     json_data    = response.json
     is_auto_init = json_data['status']
@@ -61,6 +91,10 @@ def test_is_not_auto_init(client):
 
 # Next, go through the demo initialisation then retest to see of is_auto_init == True
 def wait_for_mouse_callback(mock_setMouseCallback):
+    """
+    This function grabs the mouse_callback function once it has been set by scanbot
+    It waits a maximum of 5s (should be very quick) before timing out.
+    """
     i = 0
     timeout = 5
     while mock_setMouseCallback.call_args is None:
@@ -71,6 +105,10 @@ def wait_for_mouse_callback(mock_setMouseCallback):
     return mock_setMouseCallback.call_args[0][1]
 
 def simulate_autoInit(mock_setMouseCallback, mock_waitKey):
+    """
+    This function simulates the initialisation for automatic tip shaping.
+    It simulates clicks for the tip, sample, and metal locations.
+    """
     callback_fn = wait_for_mouse_callback(mock_setMouseCallback)
     if(callback_fn == -1):
         raise TimeoutError("Timeout while waiting for mouse callback.")
@@ -88,6 +126,9 @@ def simulate_autoInit(mock_setMouseCallback, mock_waitKey):
     time.sleep(1); mock_waitKey.return_value = 113  # ASCII value for 'q'
 
 def test_demo_init(client, tmp_path):
+    """
+    Tests that the intialisation procedure can run and completes as expected
+    """
     with patch('cv2.waitKey') as mock_waitKey, patch('cv2.VideoCapture') as mock_videoCapture, patch('cv2.imshow') as mock_imshow, patch('cv2.namedWindow'), patch('cv2.destroyAllWindows'), patch('cv2.setMouseCallback') as mock_setMouseCallback:
         mock_cap = mock_videoCapture.return_value
 
@@ -120,3 +161,179 @@ def test_demo_init(client, tmp_path):
 
         assert response.status_code == 200
         assert is_auto_init == True
+
+        """
+        Tests the move tip to sample function
+        """
+        data = {"target" : "sample",
+                "userArgs": []}
+
+        with patch('scanbot.server.scanbot.scanbot.moveTip') as mock_moveTip:
+            mock_moveTip.return_value = "Target Hit"
+
+            response = client.post('/run_go_to_target', json=data)
+
+        assert response.status_code == 200
+
+def test_auto_init_frames(client,tmp_path):
+    """
+    Test auto-tip initialisation in live mode
+    """
+    dummy_frame = np.zeros((480, 640, 3), dtype=np.uint8)
+    pil_image = Image.fromarray(dummy_frame, 'RGB')
+
+    buffered = io.BytesIO()
+    pil_image.save(buffered, format="PNG")
+    img_str = base64.b64encode(buffered.getvalue()).decode()
+
+    initialFrame = f"data:image/png;base64,{img_str}"
+    tipInFrame   = f"data:image/png;base64,{img_str}"
+
+    data = {'initialFrame': initialFrame,
+            'tipInFrame':   tipInFrame,
+            'tipLocation':  [0,0],
+            'metalLocation':[0,0],
+            'sampleLocation':[0,0]}
+
+    response = client.post('/auto_init_frames', json=data)
+
+    has_initialFrame = os.path.isfile(tmp_path / "autoinit/initialFrame.png")
+    has_tipInFrame   = os.path.isfile(tmp_path / "autoinit/tipInFrame.png")
+    has_pk           = os.path.isfile(tmp_path / "autoinit/autoinit.pk")
+
+    assert has_initialFrame
+    assert has_tipInFrame
+    assert has_pk
+
+    # Next check that the initialisation went through
+    response     = client.get('/is_auto_init')
+    json_data    = response.json
+    is_auto_init = json_data['status']
+
+    assert response.status_code == 200
+    assert is_auto_init == True
+
+    response = client.get('/get_initialised_frame')
+
+    content_disposition = response.headers.get('Content-Disposition')
+    assert 'filename=' in content_disposition
+
+    filename = content_disposition.split('filename=')[1].strip('"')
+    assert filename == 'initialisation.png'
+
+    assert response.status_code == 200
+
+    response     = client.get('/is_auto_init')
+    json_data    = response.json
+    is_auto_init = json_data['status']
+
+    assert response.status_code == 200
+    assert is_auto_init == True
+
+def test_get_config(client):
+    """
+    Test config is returned
+    """
+    response   = client.get('/scanbot_config')
+    json_data  = response.json
+    has_config = json_data['config']
+
+    assert response.status_code == 200
+    assert has_config
+
+def test_save_config(client,tmp_path):
+    """
+    Test config.ini can be saved
+    """
+    config = [{"parameter": "ip",
+               "value": ['IP Address', 'IP address of the pc controlling nanonis', 'tcp', '127.0.0.1']}]
+    data = {"config":config}
+    response = client.post('/save_config', json=data)
+    assert response.status_code == 200
+
+    config_saved = os.path.isfile(tmp_path / "scanbot_config.ini")
+    assert config_saved
+
+def test_run_survey(client,tmp_path):
+    """
+    Test surveys can run and complete
+    """
+    with patch('scanbot.server.scanbot.nanonisTCP') as mock_nanonisTCP, \
+         patch('scanbot.server.scanbot.Scan') as mock_Scan, \
+         patch('scanbot.server.scanbot.Piezo') as mock_Piezo:
+
+        dummy_frame = np.zeros((128,128))
+
+        mock_nanonisTCP.return_value.close_connection.return_value = None
+
+        mock_Scan.return_value.FrameGet.return_value      = [0,0,20e-9,20e-9,0]
+        mock_Scan.return_value.PropsGet.return_value      = ["N/A","N/A","N/A","series name","N/A"]
+        mock_Scan.return_value.BufferGet.return_value     = ["N/A","N/A",128,128]
+        mock_Scan.return_value.WaitEndOfScan.return_value = [False, "N/A", "file_path"]
+        mock_Scan.return_value.FrameDataGrab.return_value = ["N/A", dummy_frame, "N/A"]
+
+        mock_Piezo.return_value.RangeGet.return_value = [1.6e-6,1.6e-6,"N/A"]
+
+        data = {"userArgs":["-n=1","-st=0.1","-nx=1","-ny=1","-xy=10","-dx=20"]}
+        response = client.post('/run_survey', json=data)
+        time.sleep(3) # Need to wait for the survey thread to finish up
+
+        assert response.status_code == 200
+
+    data = {"timestamp":0}
+    response = client.post('/image_updates', json=data)
+    assert response.status_code == 200
+
+    content_disposition = response.headers.get('Content-Disposition')
+    assert 'filename=' in content_disposition
+
+    filename = content_disposition.split('filename=')[1].strip('"')
+    assert filename.endswith('.png')
+
+def test_run_bias_dep(client):
+    """
+    Test bias dependent imaging can run and complete
+    """
+    with patch('scanbot.server.scanbot.nanonisTCP') as mock_nanonisTCP, \
+         patch('scanbot.server.scanbot.Scan') as mock_Scan, \
+         patch('scanbot.server.scanbot.Bias') as mock_Bias, \
+         patch('scanbot.server.scanbot.ZController'):
+
+        dummy_frame = np.zeros((128,128))
+        dummy_frame[64,64] = 1
+
+        mock_nanonisTCP.return_value.close_connection.return_value = None
+
+        mock_Scan.return_value.FrameGet.return_value      = [0,0,20e-9,20e-9,0]
+        mock_Scan.return_value.PropsGet.return_value      = ["N/A","N/A","N/A","series name","N/A"]
+        mock_Scan.return_value.BufferGet.return_value     = ["N/A","N/A",128,128]
+        mock_Scan.return_value.WaitEndOfScan.return_value = [False, "N/A", "file_path"]
+        mock_Scan.return_value.FrameDataGrab.return_value = ["N/A", dummy_frame, "N/A"]
+        mock_Scan.return_value.SpeedGet.return_value      = ["N/A","N/A",0.3,"N/A","N/A","N/A"]
+
+        mock_Bias.return_value.Get.return_value = 0
+
+        data = {"userArgs":["-n=1","-px=1"]}
+        response = client.post('/run_biasdep', json=data)
+
+        time.sleep(4)
+        assert response.status_code == 200
+
+    data = {"timestamp":0}
+    response = client.post('/image_updates', json=data)
+    assert response.status_code == 200
+
+    content_disposition = response.headers.get('Content-Disposition')
+    assert 'filename=' in content_disposition
+
+    filename = content_disposition.split('filename=')[1].strip('"')
+    assert filename.endswith('.png')
+
+    response = client.get('/get_gif')
+    assert response.status_code == 200
+
+    content_disposition = response.headers.get('Content-Disposition')
+    assert 'filename=' in content_disposition
+
+    filename = content_disposition.split('filename=')[1].strip('"')
+    assert filename.endswith('.gif')