Simplified test script, fixed readme

README.md

@@ -64,7 +64,7 @@ Once all the requirements are installed, the program is ready to use. There are
 
 1. manually list filter names and parameters from command line
     ```sh
-    python3 src/main.py res/examples/Palec_P4.tif res/examples/Palec_P4.png 600 denoise_tv_chambolle iterations=1 weight=0.2 median ksize=5
+    python3 src/main.py res/examples/Palec_P4.tif res/examples/Palec_P4_from_shell.png 600 total_variation weight=0.15 median ksize=5
     ```
 
 2. from preset saved in a json config file, that can be used to tune and modify existing presetrs, or create new ones
@@ -76,7 +76,30 @@ Once all the requirements are installed, the program is ready to use. There are
 
 There is an option to input the filter series as a preset from json configuration file.
 
-```diff
+
+<style>
+  table {
+    width: 100%;
+  }
+  th, td {
+    padding: 10px;
+    font-family: monospace;
+    width: 50%;
+    vertical-align: top;
+  }
+</style>
+
+<table>
+  <thead>
+    <tr>
+      <th>General format</th>
+      <th>Woking example</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>
+        <pre><code class="language-json">
 {
     "preset": [
         {
@@ -94,11 +117,10 @@ There is an option to input the filter series as a preset from json configuratio
     ]
     ...
 }
-```
+        </code></pre>
-
+      </td>
-For example 
+      <td>
-
+        <pre><code class="language-json">
-```diff
 {
     "git_example": [
         {
@@ -112,7 +134,13 @@ For example
         }
     ]
 }
-```
+        </code></pre>
+      </td>
+    </tr>
+  </tbody>
+</table>
+
+
 
 All the filters used and their parameters are described below.
 
@@ -186,12 +214,12 @@ First optional parameter is papilar line height, second rate of curvature along
 
 * General form for curved stl generation
     ```sh
-    python3 src/main.py input_file output_file dpi --config config_file preset --stl height_line height_base curvature_x curvature_y
+    python3 src/main.py input_file output_file dpi --config config_file preset --stl c height_line height_base curvature_x curvature_y
     ```
 
 * Working example curved stl generation
     ```sh
-    python3 src/main.py res/examples/Palec_P4.tif res/examples/Palec_P4_from_preset.png 600 --config config/config.json git_example --stl 2 10 2 2
+    python3 src/main.py res/examples/Palec_P4.tif res/examples/Palec_P4_from_preset.png 600 --config config/config.json git_example --stl c 2 10 2 2
     ```
 
 # Generating planar finger model
@@ -201,21 +229,26 @@ Optional parameters are model base thickness and papilar lines height, they are
 
 * General form for planar stl generation
     ```sh
-    python3 src/main.py input_file output_file dpi --config config_file preset --stl height_line height_base -p
+    python3 src/main.py input_file output_file dpi --config config_file preset --stl p height_line height_base
     ```
 
 * Working example planar stl generation
     ```sh
-    python3 src/main.py res/examples/Palec_P4.tif res/examples/Palec_P4_from_preset.png 600 --config config/config.json git_example --stl 2 10 -p
+    python3 src/main.py res/examples/Palec_P4.tif res/examples/Palec_P4_from_preset.png 600 --config config/config.json git_example --stl p 2 10
     ```
 
 # Mapping to existing finger model
 
 This section will be added later, (if implemented) mapping of fingerprint to a given finger model.
 
+* General form for planar stl generation
+    ```sh
+    python3 src/main.py input_file output_file dpi --config config_file preset --stl m height_line height_base finger_file
+    ```
+
 # Usage
 
-usage: main.py [-h] [-m | --mirror | --no-mirror] [-p] input_file output_file dpi ([-c | --config config_file preset] | [filters ...]) [-s | --stl height_line height_base | --stl_file height_line curv_rate_x curv_rate_y]
+usage: main.py [-h] [-m | --mirror | --no-mirror] input_file output_file dpi ([-c | --config config_file preset] | [filters ...]) [-s | --stl_file p height_line height_base | --stl_file c height_line height_base curv_rate_x curv_rate_y | --stl_file m height_line height_base finger_file]
 
 Program for processing a 2D image into 3D fingerprint.
 
@@ -232,8 +265,6 @@ options:
                         switch to mirror input image
   -s [STL_FILE ...], --stl_file [STL_FILE ...]
                         create stl model from processed image
-  -p, --planar, --no-planar
-                        make stl shape planar instead of curved one
   -c CONFIG CONFIG, --config CONFIG CONFIG
                         pair: name of the config file with presets, name of the preset
 

conf/conf.json

@@ -132,11 +132,11 @@
     "git_example": [
         {
             "name": "total_variation",
-            "weight": 0.01
+            "weight": 0.15
         },
         {
             "name": "median",
-            "ksize": 3
+            "ksize": 5
         }
     ]
 }

src/test.sh

@@ -24,7 +24,7 @@ config_file=conf/conf.json
 
 # name of preset in conf. file
 #presets=("strong" "test-weak" "test-repeat" "test-strong")
-presets=("ridge" "weak")
+presets=("ridge")
 
 # generate stl files and set generation mode {"planar", "curved", "mapped"}
 generate_stl=true
@@ -43,46 +43,36 @@ apply_filter() {
     for in in ${file_arr[@]}
     do
         # check that the file exists
-        if test -f "$in"
+        [[ -f "$in" ]] || continue
-        then
-            # append preset name to filename for easier identification, if not generating stl (that would result in very long names)
-            if $generate_stl; then
-                out="${in%%${match1}*}${match1}$format"
-            else
-                out="${in%%${match1}*}_$preset${match1}$format"
-            fi
-
-            # skip stl files and files with preset name in them
-            if [[ $in == *".stl"* ]] || [[ $in == *_* ]]; then
-               ((j++))
-               continue
-            fi
-
-            ((i++))
-            echo -e "|\n|----------------------- File no. $i: $in ------------------------------|\n"
-
-            if $generate_stl; then
-                ((i++))
-                if [[ "$generate_stl_mode" = "planar" ]]; then
-                    python3 $exec_path $in $out $dpi -c $config_file $1 --stl p $height_line $height_base || break
 
-                elif [[ "$generate_stl" = "curved" ]]; then
+        # skip stl files and files with preset name in them
-                    python3 $exec_path $in $out $dpi -c $config_file $1 --stl c $height_line $height_base $curv_x $curv_y || break
+        [[ "$in" == *_* ]] && continue
+        [[ "$in" == *".stl" ]] && continue
+
+        ((i++))
+        echo -e "|\n|----------------------- File no. $i: $in ------------------------------|\n"
 
-                elif [[ "$generate_stl" = "mapped" ]]; then
+        if $generate_stl; then
-                    pass
+            out="${in%%${match1}*}${match1}$format"
+            case "$generate_stl_mode" in
+                "planar")
+                    python3 $exec_path $in $out $dpi -c $config_file $1 --stl p $height_line $height_base || break
+                    ;;
+                "curved")
+                    python3 $exec_path $in $out $dpi -c $config_file $1 --stl c $height_line $height_base $curv_x $curv_y || break
+                    ;;
+                "mapped")
                     python3 $exec_path $in $out $dpi -c $config_file $1 --stl m $height_line $height_base $fp_file|| break
-                else
+                    ;;
+                *)
                     echo "Invalid stl generation mode"
-                    break
+                    exit 1
-                fi
+                    ;;
-            else
+            esac
-                python3 $exec_path $in $out $dpi -c $config_file $1 || break
+        else
-            fi
+            out="${in%%${match1}*}_$preset${match1}$format"
-        else 
+            python3 $exec_path $in $out $dpi -c $config_file $1 || break
-            echo "File $file does not exist"
+        fi 
-        fi
-        
     done
 }