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Merged
merged 1 commit into from
Jun 12, 2021
Merged

change z scale in to scale including z,y scale. Show schema error #55

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2 changes: 1 addition & 1 deletion config/branch_metric.json
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@@ -1,7 +1,7 @@
{
"threshold_dis": 2,
"threshold_mode": 1,
"z_scale": 1,
"scale": [1, 1, 1],
"true_positive": 3,
"missed": 4,
"excess": 5
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3 changes: 1 addition & 2 deletions config/diadem_metric.json
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Expand Up @@ -7,8 +7,7 @@
"list_distant_matches": true,
"list_continuations": true,
"find_proper_root": true,
"z_scale": 1,
"TRAJECTORY_NONE": -1.0,
"scale": [1, 1, 1],
"xy_threshold": 1.2,
"z_threshold": 0.0,
"default_xy_path_error_threshold": 0.05,
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2 changes: 1 addition & 1 deletion config/length_metric.json
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Expand Up @@ -2,6 +2,6 @@
"rad_mode": 1,
"rad_threshold": 1,
"len_threshold": 0.2,
"z_scale": 1,
"scale": [1,1,1],
"debug": false
}
2 changes: 1 addition & 1 deletion config/link_metric.json
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@@ -1,3 +1,3 @@
{
"z_scale": 1
"scale": [1, 1, 1]
}
10 changes: 7 additions & 3 deletions config/schemas/branch_metric_schema.json
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Expand Up @@ -4,15 +4,19 @@
"required": [
"threshold_dis",
"threshold_mode",
"z_scale",
"scale",
"true_positive",
"missed",
"excess"
],
"properties": {
"threshold_dis": {"type": "number", "exclusiveMinimum": 0},
"threshold_dis": {"type": "number", "minimum": 0},
"threshold_mode": {"type": "number", "enum": [1, 2]},
"z_scale": {"type": "number","minimum": 0},
"scale": {"type":"array",
"additionalItems": {"type": "number", "minimum": 0},
"minItems": 3,
"maxItems": 3
},
"true_positive": {"type": "integer", "exclusiveMinimum": 0},
"missed": {"type": "integer", "exclusiveMinimum": 0},
"excess": {"type": "integer", "exclusiveMinimum": 0}
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7 changes: 5 additions & 2 deletions config/schemas/diadem_metric_schema.json
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Expand Up @@ -13,8 +13,11 @@
"list_distant_matches": {"type": "boolean", "default": "false"},
"list_continuations": {"type": "boolean", "default": "false"},
"find_proper_root": {"type": "boolean", "default": "true"},
"z_scale": {"type": "number", "minimum": 0},
"TRAJECTORY_NONE": {"type": "number"},
"scale": {"type":"array",
"additionalItems": {"type": "number", "minimum": 0},
"minItems": 3,
"maxItems": 3
},
"xy_threshold": {"type": "number", "minimum": 0},
"z_threshold": {"type": "number", "minimum": 0},
"default_xy_path_error_threshold": {"type": "number", "minimum": 0},
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12 changes: 8 additions & 4 deletions config/schemas/length_metric_schema.json
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Expand Up @@ -5,14 +5,18 @@
"rad_mode",
"rad_threshold",
"len_threshold",
"z_scale",
"scale",
"debug"
],
"properties": {
"rad_mode": {"type": "number", "enum": [1,2]},
"rad_threshold": {"type": "number", "exclusiveMinimum": 0},
"len_threshold": {"type": "number", "exclusiveMinimum": 0},
"z_scale": {"type": "number", "minimum": 0},
"rad_threshold": {"type": "number", "minimum": 0},
"len_threshold": {"type": "number", "minimum": 0},
"scale": {"type":"array",
"additionalItems": {"type": "number", "minimum": 0},
"minItems": 3,
"maxItems": 3
},
"debug": {"type": "boolean"}
}
}
8 changes: 6 additions & 2 deletions config/schemas/link_metric_schema.json
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Expand Up @@ -2,9 +2,13 @@
"title": "link metric schema",
"type": "object",
"required": [
"z_scale"
"scale"
],
"properties": {
"z_scale": {"type": "number", "minimum": 0}
"scale": {"type":"array",
"additionalItems": {"type": "number", "minimum": 0},
"minItems": 3,
"maxItems": 3
}
}
}
8 changes: 0 additions & 8 deletions config/schemas/overlap_clean_schema.json
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12 changes: 8 additions & 4 deletions config/schemas/ssd_metric_schema.json
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Expand Up @@ -5,14 +5,18 @@
"threshold_mode",
"ssd_threshold",
"up_sample_threshold",
"z_scale",
"scale",
"debug"
],
"properties": {
"threshold_mode": {"type": "integer", "enum": [1,2]},
"ssd_threshold": {"type": "number", "exclusiveMinimum": 0},
"up_sample_threshold": {"type": "number", "exclusiveMinimum": 0},
"z_scale": {"type":"number", "minimum": 0},
"ssd_threshold": {"type": "number", "minimum": 0},
"up_sample_threshold": {"type": "number", "minimum": 0},
"scale": {"type":"array",
"additionalItems": {"type": "number", "minimum": 0},
"minItems": 3,
"maxItems": 3
},
"debug": {"type": "boolean"}
}
}
3 changes: 0 additions & 3 deletions config/schemas/up_sample_schema.json
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4 changes: 2 additions & 2 deletions config/schemas/volume_metric_schema.json
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Expand Up @@ -7,8 +7,8 @@
"debug"
],
"properties": {
"length_threshold": {"type": "number", "exclusiveMinimum": 0},
"intensity_threshold": {"type": "number", "exclusiveMinimum": 0},
"length_threshold": {"type": "number", "minimum": 0},
"intensity_threshold": {"type": "number", "minimum": 0},
"debug": {"type": "boolean"}
}
}
6 changes: 3 additions & 3 deletions config/ssd_metric.json
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@@ -1,7 +1,7 @@
{
"threshold_mode": 1,
"ssd_threshold": 1,
"up_sample_threshold": 1.0,
"z_scale": 1,
"ssd_threshold": 2,
"up_sample_threshold": 1,
"scale": [1,1,1],
"debug": false
}
1 change: 0 additions & 1 deletion pyneval/cli/pyneval.py
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Expand Up @@ -240,7 +240,6 @@ def excute_metric(metric, gold_swc_tree, test_swc_tree, config, detail_dir, outp
out_path=os.path.join(detail_dir, file_name + "precision.swc"),
extra=anno_utils.get_detail_type(metric))


if output_dir:
read_json.save_json(data=result,
json_file_path=os.path.join(output_dir, file_name + ".json"))
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6 changes: 3 additions & 3 deletions pyneval/metric/branch_leaf_metric.py
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Expand Up @@ -148,10 +148,10 @@ def branch_leaf_metric(gold_swc_tree, test_swc_tree, config):
# read configs
threshold_dis = config["threshold_dis"]
threshold_mode = config["threshold_mode"]
z_scale = config["z_scale"]
scale = config["scale"]

gold_swc_tree.z_rescale(z_scale)
test_swc_tree.z_rescale(z_scale)
gold_swc_tree.rescale(scale)
test_swc_tree.rescale(scale)
# in threshold mode 2, threshold is a multiple of the average length of edges
if threshold_mode == 2:
# length of the entire gold swc forest
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6 changes: 3 additions & 3 deletions pyneval/metric/diadem_metric.py
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Expand Up @@ -940,9 +940,9 @@ def diadem_metric(gold_swc_tree, test_swc_tree, config):
diadem_init()
config_init(config)
diadam_match_utils.diadem_utils_init(config)
z_scale = config["z_scale"]
gold_swc_tree.z_rescale(z_scale)
test_swc_tree.z_rescale(z_scale)
scale = config["scale"]
gold_swc_tree.rescale(scale)
test_swc_tree.rescale(scale)
test_kdtree, test_pos_node_dict = point_match_utils.create_kdtree(test_swc_tree.get_node_list())

t_matches = {}
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6 changes: 3 additions & 3 deletions pyneval/metric/length_metric.py
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Expand Up @@ -88,11 +88,11 @@ def length_metric(gold_swc_tree, test_swc_tree, config):
rad_mode = config["rad_mode"]
rad_threshold = config["rad_threshold"]
len_threshold = config["len_threshold"]
z_scale = config["z_scale"]
scale = config["scale"]
debug = config["debug"]

gold_swc_tree.z_rescale(z_scale)
test_swc_tree.z_rescale(z_scale)
gold_swc_tree.rescale(scale)
test_swc_tree.rescale(scale)
gold_swc_tree.set_node_type_by_topo(root_id=1)
test_swc_tree.set_node_type_by_topo(root_id=5)

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6 changes: 3 additions & 3 deletions pyneval/metric/link_metric.py
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Expand Up @@ -39,9 +39,9 @@ def get_extra_pos_nodes(big_set, subset):


def link_metric(gold_swc_tree, test_swc_tree, config):
z_scale = config['z_scale']
gold_swc_tree.z_rescale(z_scale)
test_swc_tree.z_rescale(z_scale)
scale = config['scale']
gold_swc_tree.rescale(scale)
test_swc_tree.rescale(scale)

gold_list = gold_swc_tree.get_node_list()
test_list = test_swc_tree.get_node_list()
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6 changes: 3 additions & 3 deletions pyneval/metric/ssd_metric.py
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Expand Up @@ -103,10 +103,10 @@ def ssd_metric(gold_swc_tree: swc_node.SwcTree, test_swc_tree: swc_node.SwcTree,
threshold_mode = config["threshold_mode"]
ssd_threshold = config["ssd_threshold"]
up_sample_threshold = config["up_sample_threshold"]
z_scale = config["z_scale"]
scale = config["scale"]

gold_swc_tree.z_rescale(z_scale)
test_swc_tree.z_rescale(z_scale)
gold_swc_tree.rescale(scale)
test_swc_tree.rescale(scale)
u_gold_swc_tree = re_sample.up_sample_swc_tree(swc_tree=gold_swc_tree,
length_threshold=up_sample_threshold)
u_test_swc_tree = re_sample.up_sample_swc_tree(swc_tree=test_swc_tree,
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3 changes: 1 addition & 2 deletions pyneval/metric/utils/diadam_match_utils.py
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Expand Up @@ -8,7 +8,7 @@

_2D = "2d"

global TRAJECTORY_NONE
TRAJECTORY_NONE = -1.0
global g_xy_threshold
global g_z_threshold
global g_default_xy_path_error_threshold
Expand All @@ -24,7 +24,6 @@ def diadem_utils_init(config):
global g_default_z_path_error_threshold
global g_local_path_error_threshold

TRAJECTORY_NONE = config["TRAJECTORY_NONE"]
g_xy_threshold = config["xy_threshold"]
g_z_threshold = config["z_threshold"]
g_default_xy_path_error_threshold = config["default_xy_path_error_threshold"]
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6 changes: 4 additions & 2 deletions pyneval/model/swc_node.py
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Expand Up @@ -469,9 +469,11 @@ def scale(self, sx, sy, sz, adjusting_radius=True):
for tn in niter:
tn.scale(sx, sy, sz, adjusting_radius)

def z_rescale(self, z_scale):
def rescale(self, scale):
for node in self.get_node_list():
node.set_z(node.get_z() * z_scale)
node.set_z(node.get_z() * scale[2])
node.set_y(node.get_y() * scale[1])
node.set_x(node.get_x() * scale[0])

def length(self, force_update=False):
if self._total_length is not None and force_update == False:
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6 changes: 4 additions & 2 deletions setup.py
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Expand Up @@ -9,10 +9,12 @@
url='https://github.com/bennieHan/PyNeval.git',
packages=['pyneval', 'pyneval.cli', 'test', 'test.test_model',
'test.test_model.diadem_metric', 'test.test_model.length_metric',
'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model', 'pyneval.tools', 'pyneval.tools.optimize'],
'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model',
'pyneval.tools', 'pyneval.tools.optimize'],
py_modules=['pyneval', 'pyneval.cli', 'test', 'test.test_model',
'test.test_model.diadem_metric', 'test.test_model.length_metric',
'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model', 'pyneval.tools', 'pyneval.tools.optimize'],
'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model',
'pyneval.tools', 'pyneval.tools.optimize'],
data_files=[('config', glob.glob('config/*.json')),
("config/schemas", glob.glob('config/schemas/*.json'))],
install_requires=[
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