update head

compositionspace/meshes.py

@@ -1,33 +1,24 @@
 # Import libraries
 import sys
 import os
-import pandas as pd
-import h5py
-import numpy as np
-from sklearn.decomposition import PCA
-from sklearn.mixture import GaussianMixture
 import json 
 import h5py
 import numpy as np
 import pandas as pd
 import matplotlib.pylab as plt
 from tqdm import tqdm
-import os
+
+from sklearn.decomposition import PCA
+from sklearn.mixture import GaussianMixture
+from sklearn.cluster import DBSCAN, KMeans
+from sklearn.metrics import silhouette_score, homogeneity_score
+
 from pyevtk.hl import pointsToVTK
 from pyevtk.hl import gridToVTK#, pointsToVTKAsTIN
-from sklearn.cluster import DBSCAN
 from pyevtk.hl import pointsToVTK
 from pyevtk.hl import gridToVTK
 import trimesh
-from sklearn.decomposition import PCA
-from sklearn.metrics import silhouette_score
-from sklearn.cluster import KMeans
-from sklearn.mixture import GaussianMixture
-from sklearn.metrics import homogeneity_score
-#import plotly.graph_objects as go
-import numpy as np
-import h5py
-from sklearn.decomposition import PCA
+
 from scipy.spatial import Delaunay
 from functools import reduce
 
@@ -40,6 +31,7 @@ def centeroidnp(data_frame):
         sum_y = np.sum(data_frame['y'])
         sum_z = np.sum(data_frame['z'])
         return sum_x/length, sum_y/length, sum_z/length
+
 def centeroid_df(data_frame):
     length = len(data_frame['x'])
     sum_x = np.sum(data_frame['x'])

environment.yml

@@ -1,4 +1,4 @@
-name: compspace
+name: iuc09
 channels:
   - conda-forge
 dependencies:
@@ -17,3 +17,4 @@ dependencies:
   - pyvista
   - ipywidgets
   - panel
+  - trimesh

tests/Mesh_analysis.ipynb

@@ -27,37 +27,16 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "2f1898bf",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/talos/u/gazal/APT_SiGe/CompositionSpaceNFDI/tests\r\n"
-     ]
-    }
-   ],
-   "source": [
-    "MYPREFIX='/u/gazal/APT_SiGe/CompositionSpaceNFDI'\n",
-    "CWD = os.getcwd()\n",
-    "sys.path.append(MYPREFIX)\n",
-    "! echo $PWD"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
    "id": "f8a46943",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from compositionspace.datautils import Prepare_data\n",
+    "from compositionspace.datautils import DataPreparation\n",
     "import json \n",
     "import pandas as pd\n",
     "import matplotlib.pylab as plt\n",
-    "from compositionspace.segmentation import Composition_clustering\n",
-    "from compositionspace.postprocessing import Postprocess_data\n",
+    "from compositionspace.segmentation import CompositionClustering\n",
+    "from compositionspace.postprocessing import DataPostprocess\n",
     "from compositionspace.meshes import *"
    ]
   },
@@ -68,7 +47,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Vox_centroid_file = '/u/gazal/APT_SiGe/output/output_voxels/Output_voxel_cetroids_phases.h5'\n",
+    "Vox_centroid_file = 'output/output_voxels/Output_voxel_cetroids_phases.h5'\n",
     "Vox_ratios = \"/u/gazal/APT_SiGe/output/output_voxels/Output_voxel_composition.h5\"\n",
     "Slices_file = '/u/gazal/APT_SiGe/output/output_voxels/Output_big_slices.h5'\n",
     "Dbscan_results = \"/u/gazal/APT_SiGe/output/output_voxels/Output_DBSCAN_segmentation_phase_1.h5\""
@@ -249,7 +228,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

tests/experiment_params.yaml

@@ -1,4 +1,4 @@
-input_path: tests/data
+input_path: data
 output_path: output
 n_big_slices: 10
 voxel_size: 2