fix for githuworkflow

.github/workflows/publish_conda.yml

@@ -4,16 +4,34 @@ on:
   workflow_dispatch:
   release:
     types: [published]
-    
+
 jobs:
-  publish:
+  conda_deployment_with_new_tag:
+    name: Conda deployment of package with Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v1
-    - name: publish-to-conda
-      uses: MichaelsJP/conda-package-publish-action@v1.0.0
-      with:
-        subDir: 'conda-build'
-        AnacondaToken: ${{ secrets.ANACONDA_TOKEN }}
-        platforms: 'all'
-        override: true
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: conda-build/conda_build_config.yml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: Build and upload the conda packages
+        uses: uibcdf/action-build-and-upload-conda-packages@v1.3.0
+        with:
+          meta_yaml_dir: conda-build
+          python-version: ${{ matrix.python-version }}
+          platform_linux-64: true
+          platform_osx-64: true
+          platform_win-64: true
+          user: RRobert92
+          label: auto
+          token: ${{ secrets.ANACONDA_TOKEN }} # Replace with the right name of your secret

conda-build/conda_publish_env.yaml

@@ -9,7 +9,6 @@ dependencies:
   - scikit-learn>1.0.1
   - scikit-image>0.19.2
   - scipy>=1.8.1
-  - edt>=2.3.0
   - pillow>10.0.0
   - open3d>=0.9.0
   - requests>2.28.0

conda-build/meta-v0.2.2.yaml

@@ -35,7 +35,6 @@ build:
     number: 0
     script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
 
-
 about:
     home: https://github.com/SMLC-NYSBC/TARDIS
     license: MIT

docs/tutorials.rst

@@ -15,3 +15,6 @@ Tutorials
 
 `4. Visualize Instance segmentation results <usage/visualization.html>`__
 -------------------------------------------------------------------------
+
+`4. Helper functions <usage/helper.html>`__
+-------------------------------------------------------------------------

docs/usage/helper.rst

@@ -0,0 +1,2 @@
+Helper functions
+----------------

tardis_em/scripts/visualize.py

@@ -11,7 +11,7 @@
 import click
 import numpy as np
 from tardis_em.utils.visualize_pc import VisualizeFilaments, VisualizePointCloud
-from tardis_em.utils.load_data import ImportDataFromAmira
+from tardis_em.utils.load_data import ImportDataFromAmira, load_mrc_file
 from tardis_em._version import version
 
 
@@ -63,6 +63,24 @@ def main(dir_: str, _2d: bool, type_: str, animate: bool, with_node: bool):
         pc = ImportDataFromAmira(dir_).get_segmented_points()
     elif dir_.endswith(".npy"):
         pc = np.load(dir_)
+    elif dir_.endswith(".mrc"):
+        pc, _ = load_mrc_file(dir_)
+        if pc.min() == 0 and pc.max() == 1:
+            pc = np.array(np.where(pc > 0)).T
+        else:
+            idx_ = np.unique(pc)
+
+            px_df = []
+            for i in idx_:
+                if i == 0:
+                    continue
+
+                i_ = np.array(np.where(pc == i)).T
+                px_df.append(
+                    np.hstack((np.repeat(i, len(i_))[:, None], i_))
+                )
+
+            pc = np.vstack(px_df)
 
     if type_ == "p":
         if pc.shape[1] == 4 or pc.shape[1] == 3 and _2d: