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clairelbromley / ZebrafishKymographing

Various software tools written for analysis of lumen opening and membrane retraction in zebrafish.
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Error when trying to upload Exp83 E1 data #122

Open dougkelly88 opened 6 years ago

dougkelly88 commented 6 years ago

z = 240 of 413

Index exceeds matrix dimensions.

Error in detect_rhombomeres (line 90) data.edges(end).rhombomereLimits = [rotated_rhombomere_lims(1), ...

Error in on_z_pos_changed (line 22) data = detect_rhombomeres(controls, data, rhombomere_im);

Error in on_z_slice_selection_changed (line 10) on_z_pos_changed(controls.hzsl, eventdata, handles, controls);

Error in on_top_but_press (line 30) on_z_slice_selection_changed(hObject, eventdata, [], controls);

Error while evaluating uicontrol Callback

dougkelly88 commented 6 years ago

z = 166 of 362

Index exceeds matrix dimensions.

Error in detect_rhombomeres (line 90) data.edges(end).rhombomereLimits = [rotated_rhombomere_lims(1), ...

Error in on_z_pos_changed (line 22) data = detect_rhombomeres(controls, data, rhombomere_im);

Error in on_z_slice_selection_changed (line 10) on_z_pos_changed(controls.hzsl, eventdata, handles, controls);

Error in on_top_but_press (line 30) on_z_slice_selection_changed(hObject, eventdata, [], controls);

Error while evaluating uicontrol Callback

dougkelly88 commented 6 years ago

krox_20_base_script Loading files... 0 0 0 267.6427 316.7571 365.9664 430.2509 479.9677

     0

63.1888 120.9637 180.3956 229.5100 278.7193 343.0038 392.7206

z = 248 of 308

z = 250 of 308

z = 251 of 308

z = 252 of 308

z = 253 of 308

z = 254 of 308

z = 255 of 308

z = 256 of 308

z = 257 of 308

z = 258 of 308

z = 259 of 308

z = 260 of 308

z = 261 of 308

z = 262 of 308

z = 263 of 308

z = 264 of 308

z = 265 of 308

z = 266 of 308

z = 267 of 308

z = 268 of 308

z = 269 of 308

z = 270 of 308

z = 271 of 308

z = 272 of 308

z = 273 of 308

z = 274 of 308

z = 275 of 308

z = 276 of 308

z = 277 of 308

z = 278 of 308

z = 279 of 308

z = 280 of 308

z = 281 of 308

z = 282 of 308

z = 283 of 308

z = 284 of 308

z = 285 of 308

z = 286 of 308

z = 287 of 308

z = 288 of 308

z = 289 of 308

z = 290 of 308

z = 291 of 308

z = 292 of 308

z = 293 of 308

z = 294 of 308

z = 295 of 308

z = 296 of 308

z = 297 of 308

z = 298 of 308

z = 299 of 308

z = 300 of 308

z = 299 of 308

z = 298 of 308

z = 297 of 308

z = 296 of 308

z = 295 of 308

z = 294 of 308

z = 293 of 308

z = 292 of 308

z = 291 of 308

z = 290 of 308

z = 289 of 308

z = 288 of 308

z = 287 of 308

z = 288 of 308

z = 289 of 308

z = 290 of 308

z = 291 of 308

z = 292 of 308

z = 293 of 308

z = 294 of 308

z = 295 of 308

z = 296 of 308

z = 297 of 308

z = 298 of 308

z = 299 of 308

z = 300 of 308

z = 301 of 308

z = 302 of 308

z = 303 of 308

z = 302 of 308

z = 301 of 308

z = 300 of 308

299.8050

z = 195 of 308

 2

 1

z = 180 of 308

 2

 1

 2

 1

z = 165 of 308

 2

 1

Warning: loci.formats.ChannelSeparator@736916c8 is not serializable

In on_next_button_press at 17 Warning: loci.formats.ome.OMEXMLMetadataImpl@109fa047 is not serializable In on_next_button_press at 17 Warning: loci.formats.ChannelSeparator@736916c8 is not serializable In on_next_button_press at 17 Warning: loci.formats.ome.OMEXMLMetadataImpl@109fa047 is not serializable In on_next_button_press at 17 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 nonsense Warning: Directory already exists. In calc_midline_definition at 60 In calculate_output_stats at 32 In on_next_button_press at 27 nonsense Warning: Directory already exists. In calc_midline_definition at 60 In calculate_output_stats at 32 In on_next_button_press at 27 nonsense Warning: Directory already exists. In calc_midline_definition at 60 In calculate_output_stats at 32 In on_next_button_press at 27 New time point 2 of 8

New time stamp = 63.188781

z = 1 of 308

z = 276 of 314

z = 277 of 314

z = 278 of 314

z = 279 of 314

z = 280 of 314

z = 281 of 314

z = 282 of 314

z = 283 of 314

z = 284 of 314

z = 283 of 314

z = 282 of 314

z = 281 of 314

z = 280 of 314

z = 279 of 314

z = 278 of 314

z = 277 of 314

z = 278 of 314

z = 279 of 314

z = 280 of 314

z = 281 of 314

z = 282 of 314

z = 281 of 314

z = 280 of 314

z = 279 of 314

z = 278 of 314

z = 277 of 314

z = 278 of 314

z = 279 of 314

z = 280 of 314

z = 281 of 314

z = 282 of 314

z = 283 of 314

z = 284 of 314

z = 285 of 314

z = 284 of 314

z = 283 of 314

z = 282 of 314

z = 281 of 314

z = 282 of 314

z = 283 of 314

z = 284 of 314

283.7349

z = 179 of 314

 2

 1

z = 164 of 314

 2

 1

z = 149 of 314

 2

 1

Warning: loci.formats.ChannelSeparator@34f2e1df is not serializable

In on_next_button_press at 17 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: loci.formats.ome.OMEXMLMetadataImpl@17fe4577 is not serializable In on_next_button_press at 17 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: loci.formats.ChannelSeparator@34f2e1df is not serializable In on_next_button_press at 17 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: loci.formats.ome.OMEXMLMetadataImpl@17fe4577 is not serializable In on_next_button_press at 17 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 nonsense Warning: Directory already exists. In calc_midline_definition at 60 In calculate_output_stats at 32 In on_next_button_press at 27 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 nonsense Warning: Directory already exists. In calc_midline_definition at 60 In calculate_output_stats at 32 In on_next_button_press at 27 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 nonsense Warning: Directory already exists. In calc_midline_definition at 60 In calculate_output_stats at 32 In on_next_button_press at 27 In uiwait at 81 In imuitools\private\manageInteractivePlacement at 95 In imfreehand>imfreehandAPI at 171 In imfreehand>imfreehand.imfreehand at 82 In on_image_click at 10 New time point 3 of 8

New time stamp = 120.963694

z = 1 of 314

z = 2 of 314

z = 255 of 314

z = 256 of 314

z = 257 of 314

z = 258 of 314

z = 259 of 314

z = 260 of 314

z = 261 of 314

z = 262 of 314

z = 263 of 314

z = 264 of 314

z = 265 of 314

z = 266 of 314

z = 267 of 314

z = 268 of 314

z = 269 of 314

z = 270 of 314

z = 271 of 314

z = 272 of 314

z = 273 of 314

z = 274 of 314

z = 275 of 314

z = 276 of 314

z = 277 of 314

z = 278 of 314

z = 279 of 314

z = 280 of 314

z = 281 of 314

z = 282 of 314

z = 283 of 314

z = 282 of 314

z = 281 of 314

z = 280 of 314

z = 279 of 314

z = 278 of 314

z = 277 of 314

z = 278 of 314

z = 279 of 314

z = 280 of 314

z = 281 of 314

z = 282 of 314

z = 281 of 314

z = 282 of 314

z = 283 of 314

z = 284 of 314

z = 285 of 314

z = 284 of 314

z = 283 of 314

z = 282 of 314

z = 281 of 314

z = 280 of 314

z = 281 of 314

z = 282 of 314

z = 283 of 314

282.6676

z = 178 of 314

178

z = 73 of 314

73

z = -32 of 314

Error using update_image (line 8) Java exception occurred: java.lang.IllegalArgumentException: Invalid Z index: -33/314

at loci.formats.FormatTools.getIndex(FormatTools.java:468)

at loci.formats.FormatTools.getIndex(FormatTools.java:403)

at loci.formats.ChannelSeparator.getIndex(ChannelSeparator.java:262)

Error in on_z_pos_changed (line 8) update_image(controls)

Error in on_z_slice_selection_changed (line 10) on_z_pos_changed(controls.hzsl, eventdata, handles, controls);

Error in on_top_but_press (line 30) on_z_slice_selection_changed(hObject, eventdata, [], controls);

Error while evaluating uicontrol Callback

Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid Warning: loci.formats.ChannelSeparator@34f2e1df is not serializable

In on_next_button_press at 17 Warning: loci.formats.ome.OMEXMLMetadataImpl@17fe4577 is not serializable In on_next_button_press at 17 Warning: loci.formats.ChannelSeparator@34f2e1df is not serializable In on_next_button_press at 17 Warning: loci.formats.ome.OMEXMLMetadataImpl@17fe4577 is not serializable In on_next_button_press at 17 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 Error using save_images (line 26) Java exception occurred: java.lang.IllegalArgumentException: Invalid Z index: -33/314

at loci.formats.FormatTools.getIndex(FormatTools.java:468)

at loci.formats.FormatTools.getIndex(FormatTools.java:403)

at loci.formats.ChannelSeparator.getIndex(ChannelSeparator.java:262)

Error in on_next_button_press (line 24) save_images(controls, data);

Error while evaluating uicontrol Callback

Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid Warning: loci.formats.ChannelSeparator@34f2e1df is not serializable

In on_next_button_press at 17 Warning: loci.formats.ome.OMEXMLMetadataImpl@17fe4577 is not serializable In on_next_button_press at 17 Warning: loci.formats.ChannelSeparator@34f2e1df is not serializable In on_next_button_press at 17 Warning: loci.formats.ome.OMEXMLMetadataImpl@17fe4577 is not serializable In on_next_button_press at 17 Warning: Directory already exists. In save_images at 24 In on_next_button_press at 24 Error using save_images (line 26) Java exception occurred: java.lang.IllegalArgumentException: Invalid Z index: -33/314

at loci.formats.FormatTools.getIndex(FormatTools.java:468)

at loci.formats.FormatTools.getIndex(FormatTools.java:403)

at loci.formats.ChannelSeparator.getIndex(ChannelSeparator.java:262)

Error in on_next_button_press (line 24) save_images(controls, data);

Error while evaluating uicontrol Callback

Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid Warning: slider control can not have a Value outside of Min/Max range Control will not be rendered until all of its parameter values are valid

dougkelly88 commented 6 years ago

Exp86E1 T4 breaks at this timepoint

z = 192 of 401

Index exceeds matrix dimensions.

Error in detect_rhombomeres (line 90) data.edges(end).rhombomereLimits = [rotated_rhombomere_lims(1), ...

Error in on_z_pos_changed (line 22) data = detect_rhombomeres(controls, data, rhombomere_im);

Error in on_z_slice_selection_changed (line 10) on_z_pos_changed(controls.hzsl, eventdata, handles, controls);

Error in on_top_but_press (line 30) on_z_slice_selection_changed(hObject, eventdata, [], controls);

Error while evaluating uicontrol Callback