JOSS Review quick edits

Some quick edits to conform to reviewer feedback for JOSS paper.

Author: aramyxt

examples/example_1_50x50_to_model.ipynb

@@ -51,7 +51,7 @@
     "\n",
     "path = os.getcwd()\n",
     "\n",
-    "%matplotlib widget\n",
+    "%matplotlib inline\n",
     "%load_ext autoreload\n",
     "%autoreload 2"
    ]

examples/example_2_100x100_to_model.ipynb

@@ -16,6 +16,15 @@
     "Maruti K. Mudunuru"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pip install tqdm # For modules that use tdqm loading bars in notebook environments"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -37,7 +46,7 @@
     "\n",
     "path = os.getcwd()\n",
     "\n",
-    "%matplotlib widget\n",
+    "%matplotlib inline\n",
     "%load_ext autoreload\n",
     "%autoreload 2"
    ]

examples/example_3_model_properties.ipynb

@@ -16,6 +16,15 @@
     "Maruti K. Mudunuru"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pip install tqdm # For modules that use tdqm loading bars in notebook environments"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,
@@ -40,9 +49,10 @@
     "\n",
     "path = os.getcwd()\n",
     "\n",
-    "%matplotlib widget\n",
+    "%matplotlib inline\n",
     "%load_ext autoreload\n",
-    "%autoreload 2"
+    "%autoreload 2\n",
+    "os.makedirs('example_outputs', exist_ok=True) # Ensures output folder exists"
    ]
   },
   {

examples/example_4_porespy_analysis.ipynb

@@ -5,12 +5,11 @@ numpy
 opencv-python
 openpnm
 porespy
-pypardiso
 scikit-image
 scipy
 yapf
 svglib
-reportlab
+reportlab==3.6.13
 cairosvg
 gstools
 jaxlib

examples/example_5_vtk_exporting.ipynb

@@ -21,8 +21,8 @@ def network2svg(
     throat_random_debug=False,
     no_throats=False,
     middle_pores=None,
-    disconnected=None
-):  # Boolean to draw perp. lines for throat placement (debugging)
+    disconnected=None,
+    throat_vector_thres=None): # Boolean to draw perp. lines for throat placement (debugging) 
     r"""
     Create an SVG file from an OpenPNM network. 
     The network2svg function converts an OpenPNM network into an SVG image. 
@@ -210,6 +210,18 @@ def network2svg(
             pore1_coords = [pore1_x, (-pore1_y) + d2]
             pore2_coords = [pore2_x, (-pore2_y) + d2]
 
+            # If small throats are vectors
+            if throat_vector_thres is not None:
+                if generated_network['throat.diameter'][throat_index] < throat_vector_thres:
+                    design.append(
+                        dr.Line(pore1_coords[0],
+                                pore1_coords[1],
+                                pore2_coords[0],
+                                pore2_coords[1],
+                                stroke='red',
+                                stroke_width=1))
+                    continue
+
             # Distance between the two pores
             distance = math.dist(pore1_coords, pore2_coords)
 

requirements.txt

@@ -25,6 +25,7 @@ def filter_single(image,
         thresh (int): Threshold value. If not given, then Otsu's threshold is used 
         gauss (int): Radius of Gaussian Blur. Default is 5 
         invert (Boolean): Inverts pixel values of image 
+        returnthres (Boolean): Returns the threshold value calculated using Otsu 
 
     Returns:
         2D numpy array: Filtered image

src/pore2chip/export.py

@@ -12,7 +12,7 @@
 
 # Set up the module path (I am in tests folder)
 # Modify these lines if the pore2chip package is not in the PYTHONPATH
-mod_path = Path("__file__").resolve().parents[2]
+mod_path = Path(os.getcwd()).resolve().parent
 sys.path.append(os.path.abspath(mod_path))
 
 # Importing specific functions for exporting network data to SVG and DXF formats

src/pore2chip/filter_im.py

@@ -71,8 +71,6 @@ def main():
     ax[2].imshow(filtered2)
     ax[3].imshow(filtered3)
     plt.show()
-    plt.waitforbuttonpress()  # Wait for a user interaction before closing
-    plt.close()
 
     ### Advanced Tests ###
 
@@ -93,8 +91,6 @@ def main():
     ax[2].imshow(filtered_stack[1])
     ax[3].imshow(filtered_stack[2])
     plt.show()
-    plt.waitforbuttonpress()  # Wait for user interaction before closing
-    plt.close()
 
 
 if __name__ == "__main__":