PR_update (#31)

* Adding mouse mode to color surfaces/masks. Working on splitting tomogram, depending on indiviual coloring of connected triangles.

* Coloring tomogram based on segmentation

* Coloring tomogram based on segmentation

* Coloring tomogram based on segmentation

* Coloring tomogram based on segmentation

* Coloring tomogram based on segmentation

* Coloring tomogram based on segmentation works for surfaces. Next working on coloring of volume/image

* Problem is shift, is being substracted from pos and then still written out in column Origin

* Save

* Add function to color segmentation

* Add function to color segmentation

* fixed position problem, also split Angle with proper rlnAngle values, also all columns that are not numbers will still be written out

* fix selector, so that attributes that have non numerical values are excluded

* Minor debugging

* Editing flip particle function so that angles can be changed. Changing default pixelsize of particle lists that are being created from geomodels, no longer 1, but now pixelsize of currently selected particle list.

* Adding option to decide during saving of relion5, if angles should be split into rlnSubtomogram and rlnAngle and rlnAnglePrior columns should be added. Also adding help buttons to relion5 import and export widgets

* Adding option to delete particles that have the same coordinates

* Adding option to delete particles that have the same coordinates

* Minor debugging, allow to add particles to existing list, added default values for rlnAngle and rlnAnglePrior. Improved documentation.

* Minor debugging, so that non-numerical attributes are excluded from selector widget and ColorRange widget.

* Clean up

* Clean up, bug fix of selector. Adding variable to remember column order from imported relion5 star file, so that order can be used during saving.

* Adding button to select/manipulate tab

* Fixing documentation

* Bug-Fix and Clean up

* Add default pixelsize also when generating particle list from sphere.

* Improved and updated documentation.

* Include tomogram arithmetics

* Bug fix and including division

* Clean up

* Add Invert contrast button, to invert actual array values of tomogram

* Bug fix by adding default pixelsize for particle list created from geomodel. Fixing documentation

* Improve documentation.

* Improve documentation.

* Fixed the deletion, so that only particles from the same tomogram are check for neighbours within the radius.

* Improve documentation for artiax flip

* Improve documentation and fix bug for delete duplicates when no tomogram number information is available.

* Fixed geo2vol bug

* Added default, when no tomogram is provided, the currently selected one is used for scaling

* Fix documentation for "artiax moveCameraAlongLine"

* Fix documentation for "artiax generate points in/on surface"

* change layout for "Line" Geomodel tab

* fix "artiax generate points on surface"

* fix "artiax generate points on surface"

* Remove "color connected triangles" and "extract connected triangles"

---------

Co-authored-by: proth17 <p.roth@biophysik.org>

Author: proth17

bundle_info.xml

@@ -353,6 +353,12 @@ will be displayed without the ChimeraX- prefix.
     <Provider tab="ArtiaX Models" section="Change Models" mouse_mode="mask connected triangles"
       name="Mask Connected Triangles" display_name="Mask Triangles" icon="mask_triangle.png"
       description="Hides all triangles connected to the picked triangle."/>
+<!--    <Provider tab="ArtiaX Models" section="Change Models" mouse_mode="color connected triangles"-->
+<!--      name="Color Connected Triangles" display_name="Color Triangles" icon="mask_triangle.png"-->
+<!--      description="Color all triangles connected to the picked triangle."/>-->
+<!--    <Provider tab="ArtiaX Models" section="Change Models" mouse_mode="extract connected triangles"-->
+<!--      name="Extract Connected Triangles" display_name="Extract Triangles" icon="mask_triangle.png"-->
+<!--      description="Extract all triangles connected to the picked triangle and save them as a new tomogram."/>-->
 
   </Providers>
 
@@ -438,7 +444,7 @@ will be displayed without the ChimeraX- prefix.
       Creates a triangle surface between all particles marked by links.</ChimeraXClassifier>
 
     <ChimeraXClassifier>ChimeraX :: Command :: artiax flip :: General ::
-     Rotates the selected particles 180 degrees around the given axis.</ChimeraXClassifier>
+     Rotates the selected particles 180 degrees around the given axis. Default degree is 180. </ChimeraXClassifier>
 
     <ChimeraXClassifier>ChimeraX :: Command :: artiax select inside surface :: General ::
      Selects all shown particles inside the selected surface.</ChimeraXClassifier>

src/ArtiaX.py

@@ -135,6 +135,8 @@ def __init__(self, session, add: bool = True, create_managers: bool = True):
             DeletePickedTriangleMode,
             DeletePickedTetraMode,
             MaskConnectedTrianglesMode,
+            # ColorConnectedTrianglesMode,
+            # ExtractConnectedTrianglesMode
         )
 
         self.translate_selected = TranslateSelectedParticlesMode(self.session)
@@ -146,6 +148,8 @@ def __init__(self, session, add: bool = True, create_managers: bool = True):
         self.delete_picked_triangle = DeletePickedTriangleMode(self.session)
         self.delete_picked_tetra = DeletePickedTetraMode(self.session)
         self.mask_connected_triangles = MaskConnectedTrianglesMode(self.session)
+        # self.color_connected_triangles = ColorConnectedTrianglesMode(self.session)
+        # self.extract_connected_triangles = ExtractConnectedTrianglesMode(self.session)
         self.session.ui.mouse_modes.add_mode(self.translate_selected)
         self.session.ui.mouse_modes.add_mode(self.rotate_selected)
         self.session.ui.mouse_modes.add_mode(self.translate_picked)
@@ -155,6 +159,8 @@ def __init__(self, session, add: bool = True, create_managers: bool = True):
         self.session.ui.mouse_modes.add_mode(self.delete_picked_triangle)
         self.session.ui.mouse_modes.add_mode(self.delete_picked_tetra)
         self.session.ui.mouse_modes.add_mode(self.mask_connected_triangles)
+        # self.session.ui.mouse_modes.add_mode(self.color_connected_triangles)
+        # self.session.ui.mouse_modes.add_mode(self.extract_connected_triangles)
 
     @property
     def tomograms(self):
@@ -316,7 +322,6 @@ def add_particlelist(self, model):
         self.selected_partlist = model.id
         self.options_partlist = model.id
         run(self.session, "artiax clip off")
-        print("add_particlelist is being run")
 
     def add_geomodel(self, model):
         """Add a geometric model."""

src/cmd/cmd.py

@@ -283,7 +283,7 @@ def artiax_triangles_from_links(session):
     surface_from_links(session)
 
 
-def artiax_flip(session, axis=None):
+def artiax_flip(session, axis=None, angle=180):
     if not hasattr(session, "ArtiaX"):
         session.logger.warning(
             "ArtiaX is not currently running, so no particles can be reoriented."
@@ -303,7 +303,7 @@ def artiax_flip(session, axis=None):
 
     for particle in particles:
         external_axis = particle.rotation.transform_vector(axis)
-        particle.rotation = rotation(external_axis, 180) * particle.rotation
+        particle.rotation = rotation(external_axis, angle) * particle.rotation
 
     for particle_list in session.ArtiaX.partlists.iter():
         particle_list.update_places()
@@ -759,18 +759,38 @@ def artiax_gen_on_surface(session, model, method, num_pts, radius=None, exactNum
 
 
 def artiax_geomodel_to_volume(
-    session, model=None, geomodels=None, subdivide_length=None
+    session, model=None, geomodels=None, subdivide_length=None, merge=False
 ):
     from ..volume.Tomogram import Tomogram
     from chimerax.surface._surface import subdivide_mesh
     from chimerax.map_data import ArrayGridData
 
     new_model = False
+    noTomo=False
     if model is None:
-        new_model = True
-        ps = [1, 1, 1]
-        name = "segmented surfaces"
-    elif not isinstance(model, Tomogram):
+        #ps = [1, 1, 1]
+        #name = "segmented surfaces"
+        #noTomo=True
+        #model = [m for m in session.ArtiaX.tomograms.child_models() if m.visible]
+        count=0
+        for models in session.selection.models():
+            if isinstance(models, Volume):
+                print(f"found volume {models}")
+                model=models
+                count=count+1
+        if count ==0:
+            if merge == True:
+                raise UserError("Please indicate one tomogram for scaling purposes and for merging, either by command line or with the selection mouse mode.")
+            else:
+                raise UserError("Please indicate one tomogram for scaling purposes, either by command line or with the selection mouse mode.")
+        if count >=2:
+            if merge == True:
+                raise UserError("Please indicate only one tomogram for scaling purposes and merging not more.\nIf you want to combine multiple tomograms, please use the tomogram arithmetics section in ArtiaX Options Tomogram tab.")
+            else:
+                raise UserError("Please indicate only one tomogram for scaling purposes and not more.")
+        #if merge is True:
+            #raise UserError("Geomodel can not be merge with existing tomogram if it is not provided. Please indicate the tomogram.")
+    if not isinstance(model, Tomogram):
         session.logger.warning("{} is not a tomogram loaded into ArtiaX".format(model))
         return
     else:
@@ -779,10 +799,15 @@ def artiax_geomodel_to_volume(
         ps = tomo.pixelsize
         mat = tomo.data.matrix().copy()
 
+    if merge is False:
+        new_model = True
+
+
+
     if geomodels is None:
         geomodels = [g for g in session.ArtiaX.geomodels.child_models() if g.visible]
 
-    if new_model:
+    if noTomo:
         from chimerax.geometry.bounds import union_bounds
 
         union = union_bounds([gm.geometry_bounds() for gm in geomodels])
@@ -816,7 +841,7 @@ def artiax_geomodel_to_volume(
         # Set voxels
         for i, v in enumerate(vs):
 
-            if new_model:
+            if noTomo:
                 index = (v - xyz_min) / ps[0]
             else:
                 index = tomo.data.xyz_to_ijk(v)
@@ -925,6 +950,34 @@ def artiax_mask_triangles_radius(session, radius=None):
     session.ui.mouse_modes.add_mode(mct)
     run(session, 'ui mousemode right "mask connected triangles"')
 
+# def artiax_color_triangles_radius(session, radius=None):
+#     if radius is not None and radius <= 0:
+#         session.logger.warning("Select a positive radius.")
+#         return
+#     from ..mouse import ColorConnectedTrianglesMode
+#
+#     mct = session.ArtiaX.color_connected_triangles
+#     session.ui.mouse_modes.remove_mode(mct)
+#     mct = session.ArtiaX.color_connected_triangles = ColorConnectedTrianglesMode(
+#         session, radius
+#     )
+#     session.ui.mouse_modes.add_mode(mct)
+#     run(session, 'ui mousemode right "color connected triangles"')
+#
+# def artiax_extract_triangles_radius(session, radius=None):
+#     if radius is not None and radius <= 0:
+#         session.logger.warning("Select a positive radius.")
+#         return
+#     from ..mouse import ExtractConnectedTrianglesMode
+#
+#     mct = session.ArtiaX.extract_connected_triangles
+#     session.ui.mouse_modes.remove_mode(mct)
+#     mct = session.ArtiaX.extract_connected_triangles = ExtractConnectedTrianglesMode(
+#         session, radius
+#     )
+#     session.ui.mouse_modes.add_mode(mct)
+#     run(session, 'ui mousemode right "extract connected triangles"')
+
 
 def artiax_filter_tomo(
     session,
@@ -1569,6 +1622,45 @@ def artiax_user_guide(session:Session):
     raise UserError(
         "To open artiax user guide, type 'help artiax user guide'.")
 
+def artiax_delete_duplicates(session:Session, models=None, radius=0):
+
+    if not hasattr(session, "ArtiaX"):
+        session.logger.warning("ArtiaX is not currently running.")
+
+    # No Models
+    if models is None:
+        models = session.ArtiaX.partlists.child_models()
+
+    # Filter models
+    ms = []
+    for model in models:
+        # Is it a particle list?
+        from ..particle import ParticleList
+
+        if not isinstance(model, ParticleList):
+            # Is it a model that likely belongs to a particle list?
+            from chimerax.core.models import ancestor_models
+
+            if session.ArtiaX in ancestor_models([model]):
+                continue
+            else:
+                session.logger.warning(
+                    'artiax unlock: Model #{} - "{}" is not a particle list'.format(
+                        model.id_string, model.name
+                    )
+                )
+                continue
+        _id = model.id_string
+        ms.append(_id)
+
+    from ..particle.ParticleList import delete_duplicates
+
+    delete_duplicates(session,ms, radius)
+
+
+
+
+
 
 def register_artiax(logger):
     """Register all commands with ChimeraX, and specify expected arguments."""
@@ -1735,8 +1827,8 @@ def register_artiax_triangles_from_links():
 
     def register_artiax_flip():
         desc = CmdDesc(
-            optional=[("axis", AxisArg)],
-            synopsis="Rotates the selected particles 180 degrees around their y-axis.",
+            optional=[("axis", AxisArg), ("angle", FloatArg)],
+            synopsis="Rotates the selected particles. Specify the axis and degree",
             url="help:user/commands/artiax_flip.html",
         )
         register("artiax flip", desc, artiax_flip)
@@ -1821,7 +1913,7 @@ def register_artiax_gen_on_surface():
 
     def register_artiax_geomodel_to_volume():
         desc = CmdDesc(
-            optional=[("model", ModelArg)],
+            optional=[("model", ModelArg), ("merge", BoolArg)],
             keyword=[("geomodels", ListOf(ModelArg)), ("subdivide_length", FloatArg)],
             synopsis="Adds the specified geomodels to the specified volume. If no model is specified, a new one is"
             " created. If no geomodels are specified, all shown are used. The subdivide_length keyword sets"
@@ -1997,6 +2089,15 @@ def register_artiax_user_guide():
         )
         register("artiax user guide", desc, artiax_user_guide)
 
+    def register_artiax_delete_duplicates():
+        desc = CmdDesc(
+            required=[("models", Or(ModelsArg, EmptyArg))],
+            optional=[("radius", FloatArg)],
+            synopsis="Delete duplicates in particle list",
+            url="help:user/artiax_index.html",
+        )
+        register("artiax delete duplicates", desc, artiax_delete_duplicates)
+
 
     register_artiax_start()
     register_artiax_open_tomo()
@@ -2040,6 +2141,7 @@ def register_artiax_user_guide():
     register_artiax_open()
     register_artiax_save()
     register_artiax_user_guide()
+    register_artiax_delete_duplicates()
 
 
 # Possible styles

src/docs/user/artiax_index.html

@@ -48,10 +48,10 @@ <h2> <a name="top"></a> <a href="./artiax_index.html"> <img src="./ArtiaX-docs-i
       <div id="tools" class="expanded">
         <ul>
           <li><b><a href="tools/artiax.html">ArtiaX</a></b> &nbsp;– Tool for
-            Tomogram and Particle list model management.</li>
+            Tomogram, Particle list and Geometric model management.</li>
           <b></b>
           <li><b><a href="tools/artiax_options.html">ArtiaX Options</a></b>
-            &nbsp;– Tool for Tomogram and Particle list manipulation.</li>
+            &nbsp;– Tool for Tomogram, Particle list and Geometric  model manipulation.</li>
           <b></b>
           <li><b><a href="tools/artiax_toolbar.html">ArtiaX Toolbar</a></b>
             &nbsp;– ArtiaX toolbar tab.</li>
@@ -76,6 +76,8 @@ <h2> <a name="top"></a> <a href="./artiax_index.html"> <img src="./ArtiaX-docs-i
           <li><b><a href="commands/artiax_colormap.html">colormap</a></b>
             &nbsp;– set a colormap for a particle list</li>
           <b></b>
+          <li><b><a href="commands/artiax_delete_duplicate.html">delete duplicate</a></b> delete particle duplicates </li>
+          <b></b>
           <li><b><a href="commands/artiax_filter.html">filter tomo</a></b> – filter a tomogram using low, high,
           or band-pass filters </li>
           <b></b>

src/docs/user/commands/artiax_delete_duplicate.html

@@ -0,0 +1,23 @@
+<html>
+  <head>
+    <meta http-equiv="content-type" content="text/html; charset=windows-1252">
+    <link rel="stylesheet" type="text/css" href="../userdocs.css">
+    <title>Command:artiax delete duplicate</title>
+  </head>
+  <body> <a name="top"></a> <a href="../artiax_index.html"> <img src="../ArtiaX-docs-icon.svg"
+        alt="ArtiaX docs icon" class="clRight" title="User Guide Index" width="60px"></a>
+    <h3><a href="../artiax_index.html#commands">Command</a>: artiax delete duplicate</h3>
+    <h3 class="usage"><a href="usageconventions.html">Usage</a>: <br>
+      <b>artiax delete duplicate</b> [ <a href="atomspec.html#hierarchy"><i>model-spec</i></a>
+      ] [<strong>radius</strong> <i>value</i>] </h3>
+    <p> The <b>artiax delete duplicates</b> command allows deleting particle duplicates or particles that are within a specified radius (in angstrom) to each other. The particles will be sorted and processed by tomogram affiliation if they belong to multiple tomograms and this information is available. Default radius is 0. </p>
+
+    <p> Examples: </p>
+    <blockquote> <b>artiax delete duplicate #1.2.1 radius 1</b><br>
+      <b>artiax delete duplicate #1.2.1 <br>
+      </b></blockquote>
+    <p></p>
+    <hr>
+    <address>BMLS Frangakis Group / December 2024</address>
+  </body>
+</html>

src/docs/user/commands/artiax_flip.html

@@ -11,14 +11,15 @@
     class="clRight" title="User Guide Index"/></a>
     <h3><a href="../artiax_index.html#commands">Command</a>: artiax flip</h3>
     <h3 class="usage"><a href="usageconventions.html">Usage</a>:
-    <br><b>artiax flip</b> [<a href="pointspec.html#vector"><i>vector-spec</i></a>] </h3>
+    <br><b>artiax flip</b> [<a href="pointspec.html#vector"><i>vector-spec</i></a>] [<i>degree</i>] </h3>
     <p>
-    Rotates the selected particles 180 degrees around the given axis. Default axis is <strong>z</strong>.
+    Rotates the selected particles 180 degrees around the given axis x,y or z. Default axis is <strong>z</strong>. Default degree is 180.
     </p>
     <p> Examples: </p>
     <blockquote> <b>artiax flip<br>
       artiax flip x <br>
-      artiax flip 1,1,1
+      artiax flip 1,1,1 <br>
+      artiax flip y 65
       </b> </blockquote>
     <p></p>
     <hr>

src/docs/user/commands/artiax_generate_points_in_surface.html

@@ -13,7 +13,7 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>: <br>
         ts</strong> <i>value</i>]
       [<strong>radius</strong> <i>value</i>] </h3>
     <p> The <b>artiax gen in surface</b> command generates points inside the closed volume of the chosen
-    surface. Three different methods of generating points are available. Similar to the
+    surface. Three different methods of generating points are available. The pixelsize of this new particle list will be the same as for the currently activated (options selected) particle list. If no particle list is selected, the default pixelsize is 1. Similar to the
       <a href="artiax_generate_points_on_surface.html"> <i>artiax gen on surface</i></a> command.</p>
     <table style="width: 1006px; height: 380px;" border="1">
       <tbody>
@@ -42,7 +42,7 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>: <br>
         </tr>
         <tr>
           <td style="text-align: center;"><strong>radius</strong></td>
-          <td>The poisson disk radius used for the <strong>poisson</strong> method.</td>
+          <td>The poisson disk radius in angstrom used for the <strong>poisson</strong> method.</td>
           <td style="text-align: center;"><em>float</em></td>
         </tr>
       </tbody>

src/docs/user/commands/artiax_generate_points_on_surface.html

@@ -10,8 +10,8 @@ <h3><a href="../artiax_index.html#commands">Command</a>: artiax gen on surface</
     <h3 class="usage"><a href="usageconventions.html">Usage</a>: <br>
       <b>artiax gen on surface</b> <a href="atomspec.html#hierarchy"><i>model-spec</i></a>
        <i>method</i> <i>numPts</i> [<strong>radius</strong> <i>value</i>] </h3>
-    <p> The <b>artiax gene on surface</b> command generates points on the chosen surface. Two different
-      methods of generating points are available. Similar to the
+    <p> The <b>artiax gen on surface</b> command generates points on the chosen surface. Two different
+      methods of generating points are available. The pixelsize of this new particle list will be the same as for the currently activated (options selected) particle list. If no particle list is selected, the default pixelsize is 1. Similar to the
       <a href="artiax_generate_points_in_surface.html"><i>artiax gen in surface</i></a> command.</p>
     <table style="width: 1006px; height: 380px;" border="1">
       <tbody>
@@ -41,14 +41,14 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>: <br>
         </tr>
         <tr>
           <td style="text-align: center;"><strong>radius</strong></td>
-          <td>The poisson disk radius used for the <strong>poisson</strong> method.</td>
+          <td>The poisson disk radius in angstrom used for the <strong>poisson</strong> method.</td>
           <td style="text-align: center;"><em>float</em></td>
         </tr>
       </tbody>
     </table>
     <p> Examples: </p>
     <blockquote> <b>artiax gen on surface #1.3.1 uniform 100 <br>
-        artiax gen on surface #1.3.1 poisson 50 radius 10 </b> </blockquote>
+        artiax gen on surface #1.3.1 poisson 50 radius 20 </b> </blockquote>
     <p></p>
     <hr>
     <address>BMLS Frangakis Group / August 2023</address>