uhlmanngroup / splinedist

SplineDist: Automated Cell Segmentation with Spline Curves
BSD 3-Clause "New" or "Revised" License
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TypeError: function takes exactly 6 arguments (7 given) #6

Closed seekingdeep closed 2 years ago

seekingdeep commented 2 years ago

Hi there, when trying to predict using "prediction.ipynb", i am getting error in the "Prediction" step

2022-03-23 21:46:09.063463: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudnn.so.7
2022-03-23 21:46:09.955174: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcublas.so.10
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Input In [5], in <cell line: 2>()
      1 img = normalize(X[16], 1,99.8, axis=axis_norm)
----> 2 labels, details = model.predict_instances(img)

File ~/programs/splinedist/splinedist/models/base.py:446, in SplineDistBase.predict_instances(self, img, axes, normalizer, prob_thresh, nms_thresh, n_tiles, show_tile_progress, verbose, predict_kwargs, nms_kwargs, overlap_label)
    443 _shape_inst   = tuple(s for s,a in zip(_permute_axes(img).shape, _axes_net) if a != 'C')
    445 prob, dist = self.predict(img, axes=axes, normalizer=normalizer, n_tiles=n_tiles, show_tile_progress=show_tile_progress, **predict_kwargs)
--> 446 return self._instances_from_prediction(_shape_inst, prob, dist, prob_thresh=prob_thresh, nms_thresh=nms_thresh, overlap_label=overlap_label, **nms_kwargs)

File ~/programs/splinedist/splinedist/models/model2d.py:398, in SplineDist2D._instances_from_prediction(self, img_shape, prob, dist, prob_thresh, nms_thresh, overlap_label, **nms_kwargs)
    395 if overlap_label is not None: raise NotImplementedError("overlap_label not supported for 2D yet!")
    397 coord = dist_to_coord(dist, grid=self.config.grid)
--> 398 inds = non_maximum_suppression(coord, prob, grid=self.config.grid,
    399                                prob_thresh=prob_thresh, nms_thresh=nms_thresh, **nms_kwargs)
    400 labels = polygons_to_label(coord, prob, inds, shape=img_shape)
    401 # sort 'inds' such that ids in 'labels' map to entries in polygon dictionary entries

File ~/programs/splinedist/splinedist/nms.py:62, in non_maximum_suppression(coord, prob, grid, b, nms_thresh, prob_thresh, verbose, max_bbox_search)
     59 if verbose:
     60     t = time()
---> 62 survivors[ind] = c_non_max_suppression_inds(polygons.astype(np.int32),
     63                 mapping, np.float32(nms_thresh), np.int32(max_bbox_search),
     64                 np.int32(grid[0]), np.int32(grid[1]),np.int32(verbose))
     66 if verbose:
     67     print("keeping %s/%s polygons" % (np.count_nonzero(survivors), len(polygons)))

TypeError: function takes exactly 6 arguments (7 given)
seekingdeep commented 2 years ago

this issue is solved. have a look https://github.com/uhlmanngroup/splinedist/issues/2#issuecomment-976439395