Notebooks and previews

notebooks/Example_outputs/Indirect_labelling.ipynb

@@ -71,17 +71,17 @@
    "source": [
     "experiment.remove_probes()\n",
     "experiment.add_probe(\n",
-    "probe_name = \"Antibody\",\n",
+    "probe_template = \"Antibody\",\n",
     "probe_target_type = \"Sequence\",\n",
     "probe_target_value = \"ELAVGSL\",\n",
     "as_primary=True,\n",
     ")\n",
     "experiment.add_probe(\n",
-    "probe_name = \"Nanobody\",\n",
+    "probe_template = \"Nanobody\",\n",
     "probe_target_type = \"Primary\",\n",
     "probe_target_value = \"Antibody\"\n",
     ")\n",
-    "experiment.build()"
+    "experiment.build(modules=[\"particle\", \"coordinate_field\"])"
    ]
   },
   {

src/supramolsim/analysis/metrics.py

@@ -298,17 +298,20 @@ def get_circles(img,
     cirlce_params : dict
         Parameters used for circle detection.
     """
-    if blur_px:
-        gray_blurred = cv2.blur(img, (blur_px, blur_px), 0)
-    else: 
-        gray_blurred = img
+    gray_blurred = img
     if gray_blurred.min() < 0:
         gray_blurred += -gray_blurred.min()
     if gray_blurred.dtype != np.uint8:
         if gray_blurred.dtype in [np.float32, np.float64]:
-            gray_blurred = np.uint8(gray_blurred * 255)
+            #gray_blurred = np.uint8(gray_blurred * 255)
+            gray_blurred = np.uint8(gray_blurred/gray_blurred.max() * 255)
         else:
-            gray_blurred = gray_blurred.astype(np.uint8)
+            #gray_blurred = gray_blurred.astype(np.uint8)
+            gray_blurred = (gray_blurred/256).astype('uint8')
+    if blur_px:
+        gray_blurred = cv2.blur(gray_blurred, (blur_px, blur_px), 0)
+    else: 
+        gray_blurred = gray_blurred
     circles = cv2.HoughCircles(
         gray_blurred,
         cv2.HOUGH_GRADIENT,

src/supramolsim/analysis/sweep.py

@@ -71,7 +71,7 @@ def sweep_vasmples(
         probe_filepath = os.path.join(local_dir, "probes", default_probe + ".yaml")
         default_params = load_yaml(probe_filepath)
         probe_parameters = dict()
-        probe_parameters[0] = default_params
+        probe_parameters[0] = None
     if particle_defects is None:
         particle_defects = dict()
         particle_defects[0] = {"use_defects": False}

src/supramolsim/configs/parameter_settings.yaml

@@ -22,5 +22,5 @@ acquisition:
   exp_time:
     ptype: numeric
     wtype: float_slider
-    range: [0, 1, 0.001]
+    range: [0, 0.01, 0.0001]
     nintervals: 2

src/supramolsim/experiments.py

@@ -20,8 +20,14 @@
 from supramolsim.utils.io import yaml_functions
 from IPython.utils import io
 from pathlib import Path
+import sys
+
+IN_COLAB = 'google.colab' in sys.modules
+if IN_COLAB:
+    output_path = "/content/vlab4mic_outputs"
+else:
+    output_path = Path.home() / "vlab4mic_outputs"
 
-output_path = Path.home() / "vlab4mic_outputs"
 
 if not os.path.exists(output_path):
     os.makedirs(output_path)
@@ -67,12 +73,14 @@ def __post_init__(self):
         modalities_dir = os.path.join(local_dir, "modalities")
         modalities_names_list = []
         modality_parameters = {}
+        self.config_modalities = dict()
         for mods in os.listdir(modalities_dir):
             if os.path.splitext(mods)[-1] == ".yaml" and "_template" not in mods:
                 modalities_names_list.append(os.path.splitext(mods)[0])
         for mod in modalities_names_list:
-            mod_info = configuration_format.compile_modality_parameters(mod, local_dir)
+            mod_info, mod_configuration = configuration_format.compile_modality_parameters(mod, local_dir)
             modality_parameters[mod] = mod_info
+            self.config_modalities[mod] = mod_configuration
         self.local_modalities_names = modalities_names_list
         self.local_modalities_parameters = modality_parameters
         probes_dir = os.path.join(local_dir, "probes")
@@ -214,6 +222,7 @@ def update_modality(
         lateral_resolution_nm: int = None,
         axial_resolution_nm: int = None,
         psf_voxel_nm: int = None,
+        depth_of_field_nm: int = None,
         remove=False,
     ):
         """
@@ -277,6 +286,12 @@ def update_modality(
                     psf_voxel_nm,
                 ]
                 changes = True
+            if depth_of_field_nm is not None:
+                depth_in_slices = None
+                voxel_size = self.local_modalities_parameters[modality_name]["psf_params"]["voxelsize"][2]
+                depth=int(depth_of_field_nm / voxel_size)
+                self.imaging_modalities[modality_name]["psf_params"]["depth"] = depth
+                changes = True
             if changes:
                 self.imager.set_imaging_modality(
                     **self.imaging_modalities[modality_name]
@@ -822,7 +837,7 @@ def add_probe(
         probe_conjugation_target_info=None,
         probe_conjugation_efficiency: float = None,
         probe_seconday_epitope=None,
-        probe_wobbling=False,
+        probe_wobble_theta: float = None,
         labelling_efficiency: float = 1.0,
         as_primary=False,
         peptide_motif: dict = None,
@@ -931,8 +946,9 @@ def add_probe(
             probe_configuration["conjugation_efficiency"] = probe_conjugation_efficiency
         if probe_seconday_epitope is not None:
             probe_configuration["epitope_target_info"] = probe_seconday_epitope
-        if probe_wobbling:
-            probe_configuration["enable_wobble"] = probe_wobbling
+        if probe_wobble_theta is not None:
+            probe_configuration["enable_wobble"] = True
+            probe_configuration["wobble_theta"] = probe_wobble_theta
         if as_primary:
             print("Adding probe as primary linker")
             probe_configuration["as_linker"] = True
@@ -992,6 +1008,10 @@ def set_virtualsample_params(
         None
         """
         # load default configuration for virtual sample
+        try:
+            particle_minimal_distance = self.coordinate_field.molecules_params["minimal_distance"]
+        except:
+            particle_minimal_distance = None
         virtual_sample_template = os.path.join(
             self.configuration_path,
             "virtualsample",
@@ -1008,7 +1028,10 @@ def set_virtualsample_params(
             vsample_configuration["random_orientations"] = random_orientations
         if random_placing is not None:
             vsample_configuration["random_placing"] = random_placing
-        vsample_configuration["minimal_distance"] = minimal_distance
+        if minimal_distance is not None:
+            vsample_configuration["minimal_distance"] = minimal_distance
+        else:
+            vsample_configuration["minimal_distance"] = particle_minimal_distance
         self.virtualsample_params = vsample_configuration
 
     def use_image_for_positioning(

src/supramolsim/generate/labels.py

@@ -209,8 +209,6 @@ def construct_label(
     fluorophore_id: str = "AF647",
     lab_eff: float = None,
     target_info=None,
-    enable_wobble=False,
-    wobble_theta=None,
     **kwargs,
 ):
     """
@@ -230,8 +228,10 @@ def construct_label(
     # keynames reserved for parameters that can be iteratet over
     if "model_ID" in kwargs.keys():
         label_params["model"]["ID"] = kwargs["model_ID"]
-    if "distance_to_epitope" in kwargs.keys():
-        label_params["binding"]["distance"]["to_target"] = kwargs["distance_to_epitope"]
+    if "distance_to_epitope" in label_params.keys():
+        label_params["binding"]["distance"]["to_target"] = label_params["distance_to_epitope"]
+    else:
+        print("No distance to epitope provided, using default value.")
     if "distance_between_epitope" in kwargs.keys():
         label_params["binding"]["distance"]["between_targets"] = kwargs["distance_between_epitope"]
     if "paratope" in kwargs.keys():
@@ -242,9 +242,8 @@ def construct_label(
         label_params["conjugation_sites"]["efficiency"] = kwargs["conjugation_efficiency"]
     if "epitope_target_info" in kwargs.keys():
         label_params["epitope"]["target"] = kwargs["epitope_target_info"]
-    if enable_wobble:
-        if label_params["binding"]["wobble_range"]["theta"] is None:
-            label_params["binding"]["wobble_range"]["theta"] = wobble_theta
+    if "wobble_theta" in label_params.keys():
+        label_params["binding"]["wobble_range"]["theta"] = label_params["wobble_theta"]
     else:
         label_params["binding"]["wobble_range"]["theta"] = None
     ######## information about target

src/supramolsim/generate/molecular_structure.py

@@ -853,7 +853,7 @@ def show_target_labels(
             fig.show
 
     def show_assembly_atoms(
-        self, assembly_fraction=0.01, view_init=[0, 0, 0], axesoff=True
+        self, assembly_fraction=0.01, view_init=[0, 0, 0], axesoff=True,return_plot=False
     ):
         """
         Visualize a fraction of the assembly atoms.
@@ -888,7 +888,11 @@ def show_assembly_atoms(
         )
         if axesoff:
             ax.set_axis_off()
-        return fig
+        if return_plot:
+            plt.close()
+            return fig
+        else:
+            fig.show()
 
     def create_instance_builder(self, write=False, savingdir=None):
         """