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.travis.yml has changed.

@@ -423,7 +423,7 @@
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423 423
            title = subject_id
424 424
        self.subject_id = subject_id
425 425
426 -
        if not isinstance(views, list):
426 +
        if not isinstance(views, (list, tuple)):
427 427
            views = [views]
428 428
        n_row = len(views)
429 429
@@ -1095,15 +1095,13 @@
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1095 1095
            smooth_mat = None
1096 1096
1097 1097
        magnitude = None
1098 -
        magnitude_max = None
1099 1098
        if array.ndim == 3:
1100 1099
            if array.shape[1] != 3:
1101 1100
                raise ValueError('If array has 3 dimensions, array.shape[1] '
1102 1101
                                 'must equal 3, got %s' % (array.shape[1],))
1103 1102
            magnitude = np.linalg.norm(array, axis=1)
1104 1103
            if scale_factor is None:
1105 -
                distance = np.sum([array[:, dim, :].ptp(axis=0).max() ** 2
1106 -
                                   for dim in range(3)])
1104 +
                distance = 4 * np.linalg.norm(array, axis=1).max()
1107 1105
                if distance == 0:
1108 1106
                    scale_factor = 1
1109 1107
                else:
@@ -1111,7 +1109,6 @@
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1111 1109
                                    (4 * array.shape[0] ** (0.33)))
1112 1110
            if self._units == 'm':
1113 1111
                scale_factor = scale_factor / 1000.
1114 -
            magnitude_max = magnitude.max()
1115 1112
        elif array.ndim not in (1, 2):
1116 1113
            raise ValueError('array has must have 1, 2, or 3 dimensions, '
1117 1114
                             'got (%s)' % (array.ndim,))
@@ -1188,7 +1185,7 @@
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1188 1185
            if brain['hemi'] == hemi:
1189 1186
                s, ct, bar, gl = brain['brain'].add_data(
1190 1187
                    array, min, mid, max, thresh, lut, colormap, alpha,
1191 -
                    colorbar, layer_id, smooth_mat, magnitude, magnitude_max,
1188 +
                    colorbar, layer_id, smooth_mat, magnitude,
1192 1189
                    scale_factor, vertices, vector_alpha, **kwargs)
1193 1190
                surfs.append(s)
1194 1191
                bars.append(bar)
@@ -2115,13 +2112,11 @@
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2115 2112
                    if vectors is not None:
2116 2113
                        vectors = vectors[:, :, time_idx]
2117 2114
2118 -
                vector_values = scalar_data.copy()
2119 2115
                if data['smooth_mat'] is not None:
2120 2116
                    scalar_data = data['smooth_mat'] * scalar_data
2121 2117
                for brain in self.brains:
2122 2118
                    if brain.hemi == hemi:
2123 -
                        brain.set_data(data['layer_id'], scalar_data,
2124 -
                                       vectors, vector_values)
2119 +
                        brain.set_data(data['layer_id'], scalar_data, vectors)
2125 2120
                del brain
2126 2121
                data["time_idx"] = time_idx
2127 2122
@@ -3225,24 +3220,25 @@
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3225 3220
        self._mesh_clones.pop(array_id).remove()
3226 3221
        self._mesh_dataset.point_data.remove_array(array_id)
3227 3222
3228 -
    def _add_vector_data(self, vectors, vector_values, fmin, fmid, fmax,
3229 -
                         scale_factor_norm, vertices, vector_alpha, lut):
3223 +
    def _add_vector_data(self, vectors, fmin, fmid, fmax,
3224 +
                         scale_factor, vertices, vector_alpha, lut):
3230 3225
        vertices = slice(None) if vertices is None else vertices
3231 3226
        x, y, z = np.array(self._geo_mesh.data.points.data)[vertices].T
3232 3227
        vector_alpha = min(vector_alpha, 0.9999999)
3233 3228
        with warnings.catch_warnings(record=True):  # HasTraits
3234 3229
            quiver = mlab.quiver3d(
3235 3230
                x, y, z, vectors[:, 0], vectors[:, 1], vectors[:, 2],
3236 -
                scalars=vector_values, colormap='hot', vmin=fmin,
3231 +
                colormap='hot', vmin=fmin, scale_mode='vector',
3237 3232
                vmax=fmax, figure=self._f, opacity=vector_alpha)
3238 3233
3239 3234
        # Enable backface culling
3240 3235
        quiver.actor.property.backface_culling = True
3241 3236
        quiver.mlab_source.update()
3242 3237
3243 -
        # Compute scaling for the glyphs
3244 -
        quiver.glyph.glyph.scale_factor = (scale_factor_norm *
3245 -
                                           vector_values.max())
3238 +
        # Set scaling for the glyphs
3239 +
        quiver.glyph.glyph.scale_factor = scale_factor
3240 +
        quiver.glyph.glyph.clamping = False
3241 +
        quiver.glyph.glyph.range = (0., 1.)
3246 3242
3247 3243
        # Scale colormap used for the glyphs
3248 3244
        l_m = quiver.parent.vector_lut_manager
@@ -3293,7 +3289,7 @@
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3293 3289
3294 3290
    @verbose
3295 3291
    def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
3296 -
                 colorbar, layer_id, smooth_mat, magnitude, magnitude_max,
3292 +
                 colorbar, layer_id, smooth_mat, magnitude,
3297 3293
                 scale_factor, vertices, vector_alpha, **kwargs):
3298 3294
        """Add data to the brain"""
3299 3295
        # Calculate initial data to plot
@@ -3308,7 +3304,6 @@
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3308 3304
            array_plot = magnitude[:, 0]
3309 3305
        else:
3310 3306
            raise ValueError("data has to be 1D, 2D, or 3D")
3311 -
        vector_values = array_plot
3312 3307
        if smooth_mat is not None:
3313 3308
            array_plot = smooth_mat * array_plot
3314 3309
@@ -3316,16 +3311,13 @@
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3316 3311
        array_plot = _prepare_data(array_plot)
3317 3312
3318 3313
        array_id, pipe = self._add_scalar_data(array_plot)
3319 -
        scale_factor_norm = None
3320 3314
        if array.ndim == 3:
3321 -
            scale_factor_norm = scale_factor / magnitude_max
3322 3315
            vectors = array[:, :, 0].copy()
3323 3316
            glyphs = self._add_vector_data(
3324 -
                vectors, vector_values, fmin, fmid, fmax,
3325 -
                scale_factor_norm, vertices, vector_alpha, lut)
3317 +
                vectors, fmin, fmid, fmax,
3318 +
                scale_factor, vertices, vector_alpha, lut)
3326 3319
        else:
3327 3320
            glyphs = None
3328 -
        del scale_factor
3329 3321
        mesh = pipe.parent
3330 3322
        if thresh is not None:
3331 3323
            if array_plot.min() >= thresh:
@@ -3364,7 +3356,7 @@
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3364 3356
3365 3357
        self.data[layer_id] = dict(
3366 3358
            array_id=array_id, mesh=mesh, glyphs=glyphs,
3367 -
            scale_factor_norm=scale_factor_norm)
3359 +
            scale_factor=scale_factor)
3368 3360
        return surf, orig_ctable, bar, glyphs
3369 3361
3370 3362
    def add_annotation(self, annot, ids, cmap, **kwargs):
@@ -3475,7 +3467,7 @@
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3475 3467
        self._remove_scalar_data(data['array_id'])
3476 3468
        self._remove_vector_data(data['glyphs'])
3477 3469
3478 -
    def set_data(self, layer_id, values, vectors=None, vector_values=None):
3470 +
    def set_data(self, layer_id, values, vectors=None):
3479 3471
        """Set displayed data values and vectors."""
3480 3472
        data = self.data[layer_id]
3481 3473
        self._mesh_dataset.point_data.get_array(
@@ -3492,12 +3484,12 @@
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3492 3484
3493 3485
            # Update glyphs
3494 3486
            q.mlab_source.vectors = vectors
3495 -
            q.mlab_source.scalars = vector_values
3496 3487
            q.mlab_source.update()
3497 3488
3498 3489
            # Update changed parameters, and glyph scaling
3499 -
            q.glyph.glyph.scale_factor = (data['scale_factor_norm'] *
3500 -
                                          values.max())
3490 +
            q.glyph.glyph.scale_factor = data['scale_factor']
3491 +
            q.glyph.glyph.range = (0., 1.)
3492 +
            q.glyph.glyph.clamping = False
3501 3493
            l_m.load_lut_from_list(lut / 255.)
3502 3494
            l_m.data_range = data_range
3503 3495
Files Coverage
surfer 75.02%
Project Totals (7 files) 75.02%
685.2
TRAVIS_OS_NAME=linux
fk8evi6rt77ycopj
Untitled
685.1
TRAVIS_OS_NAME=linux
685.3
TRAVIS_OS_NAME=osx
1
coverage:
2
  precision: 2
3
  round: down
4
  range: "70...100"
5
  status:
6
    project:
7
      default:
8
        target: auto
9
        threshold: 0.01
10
    patch: false
11
    changes: false
12
comment:
13
  layout: "header, diff, sunburst, uncovered"
14
  behavior: default
Sunburst
The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file. The size and color of each slice is representing the number of statements and the coverage, respectively.
Icicle
The top section represents the entire project. Proceeding with folders and finally individual files. The size and color of each slice is representing the number of statements and the coverage, respectively.
Grid
Each block represents a single file in the project. The size and color of each block is represented by the number of statements and the coverage, respectively.
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