linnarsson-lab / FISHscale

Spatial analysis of FISH data
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multi dataset visualisation #14

Closed simone-codeluppi closed 2 years ago

simone-codeluppi commented 3 years ago

I loaded the files in the current folder https://www.dropbox.com/sh/fr93kei4ts6j4j2/AADiO0lMlHR6EZ6L4a6_6LTWa?dl=0 and when I run the md.visualize() command I get the following error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/var/folders/3j/qdw444h57j5b6vr3jmttjvs80000gp/T/ipykernel_35034/2806952897.py in <module>
----> 1 md.visualize()

~/Github_code/FISHscale/utils/dataset.py in visualize(self, columns, width, height, show_axis, color_dic, x, y, c)
    697             color_dic = self.color_dict
    698 
--> 699         window = Window(self,
    700                         columns,
    701                         width,

~/Github_code/FISHscale/visualization/primitiveVis_open3dv2.py in __init__(self, dataset, columns, width, height, show_axis, x_alt, y_alt, c_alt, plot_type)
    100             for x in self.dataset:
    101                 self.dic_pointclouds['File'].append(str(x.filename))
--> 102             self.pass_multi_data()
    103 
    104         self.show_axis= show_axis

~/Github_code/FISHscale/visualization/primitiveVis_open3dv2.py in pass_multi_data(self)
    159 
    160         if self.c_alt != {}:
--> 161             for c in self.c_alt:
    162                 #unique_ca = np.unique(self.c_alt[c])
    163                 self.dic_pointclouds[c]= self.c_alt[c]

TypeError: 'NoneType' object is not iterable
larsborm commented 2 years ago

Alejandro fixed it.