Added scripts to measure the length of rectangle ROIs

README.md

@@ -1,5 +1,5 @@
 # Microscope-Measurement-Tools
-Microscope Measurement plugin for [FIJI](http://fiji.sc).
+Microscope Measurement plugin for [FIJI](http://fiji.sc)
 
 This set of [FIJI](http://fiji.sc) plugins provides a quick way to save distance/length calibrations for various microscopes/objectives in a simple text file, and then draw calibrated distances onto your images.
 
@@ -19,7 +19,7 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated
 1. Download and install the [scientific image analysis program FIJI](http://fiji.sc)
 1. Download the most recent [Microscope Tools Release from Github](https://github.com/Elaniobro/Microscope-Measurement-Tools/releases/tag/v2.4)
     1. Extract/Unzip the file you downloaded from Github called: `Microscope-Measurment-tools`
-    1. Move the folder into the FIJI plugins directory on your MacOS
+    1. Move the folder contents (or just the plugins and macros directories) into the FIJI directory (Fiji.app). When prompted, choose to overwrite the file StartupMacros.fiji.ijm
     <img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/pkg_contents.png?raw=true" width="600"/>
 
 **note** _MacOS may prevent you from opening an unverified application follow steps below to open_
@@ -30,68 +30,72 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated
 ## ⚖️ Calibration
 1. Take photos of a known measurment sample with your microscope, at each magnification you want to calibrate
 1. Open FIJI
-1. Open an image file taken at the desired maginification with a measurment marker. e.g. Open a photo of your micrometer slide taken with your 40x objective
-1. Zoom in on the photo to view the micrometer scale
+1. Open an image file taken at the desired maginification with a measurment marker. e.g. Open a photo of a micrometer slide
+1. Zoom in on the photo to view the scale
 1. Draw a line `ROI` (Region Of Interest) along the calibration measurment feature. e.g. along the micrometer <img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/roi.png?raw=true" width="600"/>
 1. Navigate to and select `Analyze > Set Scale`
 1. The "Distance in Pixels" will already be set by your line ROI
-1. Type in the "Known Distance" from your measurement feature, mine is 5μm <img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/set_scale.png?raw=true" width="600"/>
-1. Record the resulting "Scale" value, e.g. 31.1716 pixel/unit, where unit is cm, mm, μm, etc
-1. The "Scale" value will be used in your `Microscope_Calibrations_user_settings.py` file, so recored both a name and the scale value. e.g:
-    ```
-    Swift 350T 4x: 0.9058 px/μm
-    Swift 350T 10x: 1.81 px/μm
-    Swift 350T 40X: 12.5455 px/μm
-    Swift 350T 100X: 31.1716 px/μm
-    ```
-    **_these are just dummy values_**
-1. Open up `/Applications/Fiji.app/plugins/Analyze/Microscope Measurement Tools/Microscope_Calibrations_user_settings.py` in your IDE (Integrated Deelopment Environment)
-1. Edit the `names` list to reflect the name of each calibration on line 21:
-      ```
-      names = [
-        'Swift 350T 4x',
-        'Swift 350T 10x',
-        'Swift 350T 40x',
-        'Swift 350T 100x',
-      ]
-      ```
-1. Edit the `cals` list to reflect the corresponding `pixel-per-unit` calibration for each setting, from your previous records, on line 30:
-      ```
-      cals = [
-        0.9058,
-        1.81,
-        12.5455,
-        31.1716,
-      ]
-      ```
-1. Quit FIJI
-1. Re-start the FIJI application. This will allow the application to register the changes you made to the plugin
-**note** _for any subsquent changes, you will have to save the file, quit the application and re-open it to see the changes_
-1. Open an image
-1. Run `Analyze > Microscope Measurment Tools > Choose Microscope Calibration` and see a pop-up window that shows the new names and calibration values you set in `Microscope_Calibrations_user_settings.py`. <img src="https://raw.githubusercontent.com/Elaniobro/Microscope-Measurement-Tools/master/img/microscope_calibrations.png" width="600"/>
-1. You may also apply the same scale and scale bar to all images you have open, but selecting the checkboxes. Doing so will open another pop-up, where you can see how the scale will look. In the example below, the bar is set to 10μm, white text and placed in the lower right corner 
-<img src="https://raw.githubusercontent.com/Elaniobro/Microscope-Measurement-Tools/master/img/scale_bar.png" width="600"/>
+1. Type in the "Known Distance" from your measurement feature <img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/set_scale.png?raw=true" width="600"/>
+1. (Optional) Check 'Global' to apply this same scale to all images opened during this session
+1. (Optional) Add the scale as a preset that can be accessed at Plugins\Analyze\Microscope Measurement Tools\Choose Microscope Calibration (F1)
+    1. Record the resulting "Scale" value, e.g. 31.1716 pixel/unit, where unit is cm, mm, μm, etc
+    1. The "Scale" value will be used in your `Microscope_Calibrations_user_settings.py` file, so recored both a name and the scale value. e.g:
+        ```
+        Swift 350T 4x: 0.9058 px/μm
+        Swift 350T 10x: 1.81 px/μm
+        Swift 350T 40X: 12.5455 px/μm
+        Swift 350T 100X: 31.1716 px/μm
+        ```
+        **_these are just dummy values_**
+    1. Open up `/Fiji.app/plugins/Analyze/Microscope Measurement Tools/Microscope_Calibrations_user_settings.py` in your preferred text editor or python IDE
+    1. Edit the `names` list to reflect the name of each calibration on line 21:
+          ```
+          names = [
+            'Swift 350T 4x',
+            'Swift 350T 10x',
+            'Swift 350T 40x',
+            'Swift 350T 100x',
+          ]
+          ```
+    1. Edit the `cals` list to reflect the corresponding `pixel-per-unit` calibration for each setting, from your previous records, on line 30:
+          ```
+          cals = [
+            0.9058,
+            1.81,
+            12.5455,
+            31.1716,
+          ]
+          ```
+    1. Save the file, and delete the file "Microscope_Calibrations_user_settings$py.pyclass" (if present)
+    1. Quit FIJI
+    1. Re-start the FIJI application. This will allow the application to register the changes you made to the plugin
+    **note** _for any subsquent changes, you will have to repeat the last three steps to see the changes_
 
 ## 📈 Usage
-Three files are included, which will show up in your FIJI "Analyze" menu:
+Several files are included, which will show up at Plugins\Analyze\Microscope Measurement Tools. Shortcuts are also added to the tool bar.
 
 + **Choose_Microscope_Calibration.py**
-  + *Opens the "Choose Calibration" window, for setting the measurement scale to a preconfigured value.*
+  + *Opens the "Choose Calibration" window, for setting the measurement scale to a preconfigured value (hotkey F1)*
 + **Draw_Measurement_-_Line.py**
-  + *Converts a Line ROI into a drawn annotation with the measurement length indicated.*
+  + *Converts a Line ROI into a drawn annotation with the measurement length indicated*
++ **Draw_Rectangle_Long_Length.py**
+  + *Adds a drawn annotation of the length of a rectangle ROI along the long side (hotkey 'q')*
++ **Draw_Rectangle_Short_Length.py**
+  + *Adds a drawn annotation of the length of a rectangle ROI along the short side (hotkey 'g')*
++ **Draw_Rectangle_Length_x_Width.py**
+  + *Adds a drawn annotation of the length and width of a rectangle ROI (hotkey 'u')*
 
 + **Microscope_Calibrations_user_settings.py**
   + *User-editable Settings file that contains your pre-configured scale calibrations, along with settings for drawing annotations (background/text color etc.)*
 
 View the [How-To Calibrate an Ocular Micrometer](https://www.youtube.com/watch?v=HaqgCtA-ioI&t=738s)
 
 ## 📐 Making + Drawing measurements
-Select the Menu Item `Plugins > Analyze > Microscope Measurement Tools > Choose Microscope Calibration`, and select your microscope/objective from the resulting list.  The pixel scale will be applied.
+(Recommended) Set a scale either manually using the procedure outlined in the 'Calibration' Section, or from the presets by going to `Plugins > Analyze > Microscope Measurement Tools > Choose Microscope Calibration` (F1)
 
-You can now drag a Line (or other type of ROI) on any feature, and the FIJI toolbar will show you the measurement dynamically.  Other FIJI functions can now also be used for calibrated measurements (areas etc.).
-
-To draw this measurement on your image, drag the Line to the desired location, and select the menu item `Plugins > Analyze > Microscope Measurement Tools > Draw Measurement - Line`
+You can now drag a Line or Rectangle (or other type of ROI) on any feature, and the FIJI toolbar will show you the measurement dynamically.  Other FIJI functions can now also be used for calibrated measurements (areas etc.).
 
+To draw this measurement on your image, drag the Line or Rectangle at the desired location, and select the desired measurement from `Plugins > Analyze > Microscope Measurement Tools`, click the toolbar icon, or type the hotkey (details for each measurement option are in 'Usage' section)
 
 ## 🔧 Custom Calibration Functions
 A custom function can be added to the list of available calibrations (as opposed to a static scale value).  A sub-folder is included showing an example of how to do this. The example is for a JEOL SEM (scanning electron microscope), and the example function will determine the scale of the SEM image by parsing an accompanying text file.