Merge pull request imcf#146 from rohangirishrao/interactive-tests-fix

Add clear expected results for interactive Fiji-tests (Issue imcf#144)

Author: ehrenfeu

tests/interactive-imagej/shading-test.md

@@ -7,8 +7,15 @@
 #@ CommandService command
 #@ LogService sjlog
 
-import os
+# Prerequisites before running this script in Fiji:
+#
+# - Drag and drop, and run this script in Fiji.
+# - Set parameters in the dialog box.
+#
+# Expected result: a file named "script_parameters.txt" is written to the
+# chosen output directory, with all parameters from the script.
 
+import os
 import imcflibs.log
 from imcflibs.imagej import misc
 

…ractive-imagej/save-script-parameters.py …ve-imagej/test_save_script_parameters.pytests/interactive-imagej/save-script-parameters.py renamed to tests/interactive-imagej/test_save_script_parameters.py tests/interactive-imagej/save-script-parameters.py renamed to tests/interactive-imagej/test_save_script_parameters.py

@@ -1,29 +1,24 @@
-# Test the send_notification_email function
+# Prerequisites before running this script in Fiji:
+#
+# Add the following lines to IJ_Prefs.txt:
+#   Linux/Mac: ~/.imagej/IJ_Prefs.txt
+#   Windows:   C:\Users\<USERNAME>\.imagej\IJ_Prefs.txt
+#
+#   .imcf.sender_email=imcf@unibas.ch
+#   .imcf.smtpserver=smtp.unibas.ch
+#
+# Expected result: a mail is sent to nikolaus.ehrenfeuchter@unibas.ch from
+# imcf@unibas.ch, with a print statement in Fiji.
 
-```Python
 from imcflibs.imagej.misc import send_notification_email
 
 from imcflibs.log import LOG as log
 from imcflibs.log import enable_console_logging
 from imcflibs.log import set_loglevel
 
-
-"""
-Usage:
-BEFORE starting Fiji, add to the IJ_Prefs.txt:
-
-.imcf.sender_email=imcf@unibas.ch
-.imcf.smtpserver=smtp.unibas.ch
-
-Linux/Mac: ~/.imagej/IJ_Prefs.txt 
-Windows: C:\Users\<USERNAME>\.imagej\IJ_Prefs.txt
-"""
-
-
 enable_console_logging()
 set_loglevel(2)
 
-
 # see if logging works:
 log.warn("warn")
 log.debug("DEBUG")
@@ -36,4 +31,3 @@
 )
 
 log.info("DONE")
-```

…active-imagej/send-notification-email.md …e-imagej/test_send_notification_email.pytests/interactive-imagej/send-notification-email.md renamed to tests/interactive-imagej/test_send_notification_email.py tests/interactive-imagej/send-notification-email.md renamed to tests/interactive-imagej/test_send_notification_email.py

@@ -0,0 +1,17 @@
+# Prerequisites before running this script in Fiji:
+#
+# - Open an image to test on (e.g. Shaded-blobs.png) in Fiji before running.
+# - Drag this script into Fiji and run it.
+#
+# Expected result: a new image titled "Result of blobs.gif" opens alongside
+# the original, showing a flatfield corrected version of the raw blobs.gif.
+
+from imcflibs.imagej import shading
+import ij
+from ij import IJ
+
+imp = IJ.getImage()
+
+# Any other method in class shading also works
+imcf_shading = shading.simple_flatfield_correction(imp)
+imcf_shading.show()

tests/interactive-imagej/test_shading.py

@@ -1,17 +1,13 @@
-# Testing the `imcflibs.imagej.trackmate` module
+# Prerequisites before running this script in Fiji:
+#
+# - Open the blobs image, e.g. using Ctrl + Shift + B.
+# - Drag and drop this script and run it in Fiji.
+#
+# Expected result: a label image named "LblImg_blobs.gif" opens next to the raw
+# blobs.gif with many segmented spots (LoG detector). With the Cellpose detector
+# the segmented blobs should be quite accurate; the LoG detector finds many spots
+# across the image.
 
-Instructions for *interactive* testing (i.e. manually running a script in Fiji's
-*Script Editor*) of the `imcflibs.imagej.trackmate` module.
-
-## Testing instructions
-
-1. An updated `python-imcflibs.jar` containing the changes to be tested has to
-   be installed into Fiji already.
-1. Next, open the blobs image, e.g. using `Ctrl` + `Shift` + `B`.
-1. Then, launch the *Script Editor* using `Ctrl` + `Shift` + `N`, paste the
-   following script and finally run it:
-
-```Python
 from imcflibs.imagej import trackmate
 from ij import IJ
 
@@ -33,8 +29,3 @@
 
 res_img = trackmate.run_trackmate(imp, settings)
 res_img.show()
-```
-
-## Expected behavior / results
-
-FIXME!!