test_localize fix

jungmannlab · Feb 17, 2023 · ddc98e2 · ddc98e2
1 parent 2f285fa
commit ddc98e2
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/picasso/__main__.py b/picasso/__main__.py
@@ -779,7 +779,10 @@ def _localize(args):
             raise Exception("GPUfit not installed. Aborting.")
 
     for index, element in enumerate(vars(args)):
-        print("{:<8} {:<15} {:<10}".format(index + 1, element, getattr(args, element)))
+        try:
+            print("{:<8} {:<15} {:<10}".format(index + 1, element, getattr(args, element)))
+        except TypeError: # if None is default value
+            print("{:<8} {:<15} {}".format(index + 1, element, "None"))
     print("------------------------------------------")
 
     def check_consecutive_tif(filepath):
@@ -848,6 +851,7 @@ def prompt_info():
                 save_info(info_path, [info])
 
     if paths:
+        print(args)
         box = args.box_side_length
         min_net_gradient = args.gradient
         roi = args.roi

diff --git a/tests/data/testdata_locs.hdf5 b/tests/data/testdata_locs.hdf5
diff --git a/tests/data/testdata_locs.yaml b/tests/data/testdata_locs.yaml
@@ -65,8 +65,10 @@ Structure.StructureY: 0,20,40,60,0,20,40,60,0,20,40,60
 Width: 32
 ---
 Box Size: 7
-Fit method: LQ, Gaussian
+Convergence Criterion: 0.001
+Fit method: mle
 Generated by: Picasso Localize
-Min. Net Gradient: 3000
+Max. Iterations: 1000
+Min. Net Gradient: 5000
 Pixelsize: 130
 ROI: null
diff --git a/tests/test_localize.py b/tests/test_localize.py
@@ -27,6 +27,7 @@ def test_localize():
     args.sensitivity = 1
     args.gain = 1
     args.qe = 1
+    args.roi = None
     args.drift = 100
 
     for fit_method in ["mle"]: