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Fix APs and display stack

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This commit is contained in:
Florent Guiotte 2018-04-16 12:49:32 +02:00
parent 8e4e6e0ef4
commit 747491d36d
4 changed files with 86 additions and 22 deletions
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2
Notebooks/APs.ipynb
View File

@ -157,7 +157,7 @@
"sd = np.array([0.5,0.9,0.99,0.999])#,1e4,1e5,5e5])\n",
"moi = np.array([0.01,0.02,0.03,0.04,0.05,0.06,0.07,0.08,0.09,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,0.99])\n",
"\n",
"t = triskele.Triskele(layers_stack[:,:,0], verbose=False)\n",
"t = triskele.Triskele(layers_stack[:,:,:2], verbose=False)\n",
"attributes_min = t.filter(tree='min-tree',\n",
" area=area,\n",
" standard_deviation=sd,\n",

49
Notebooks/Node Streaming Benchmark.ipynb
View File

@ -24,15 +24,13 @@
"metadata": {},
"outputs": [],
"source": [
"load = ld2dap.LoadTIFF(('../Data/test.tiff', '../Data/test2.tiff'))\n",
"load = ld2dap.LoadTIFF('../Data/phase1_rasters/DEM_C123_TLI/UH17_GEG05_TR.tif')\n",
"trsh = ld2dap.Treshold(1e4)\n",
"aps = ld2dap.AttributeProfiles(area=[100, 1e3, 1e4])\n",
"aps2 = ld2dap.AttributeProfiles(area=[100, 1e3, 1e4])\n",
"aps = ld2dap.AttributeProfiles(area=[1e6], moi=[.5])\n",
"\n",
"disp = ld2dap.ShowFig(fname=None)\n",
"disp = ld2dap.ShowFig('all')\n",
"out = ld2dap.RawOutput()\n",
"\n",
"aps2.input = aps\n",
"out.input = aps\n",
"disp.input = aps\n",
"aps.input = trsh\n",
@ -41,6 +39,15 @@
"disp.run()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"' > '.join(x if x is not None else '' for x in out.metadata[0].desc[3])"
]
},
{
"cell_type": "code",
"execution_count": null,
@ -50,14 +57,20 @@
"out.data.shape"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"for i, m in enumerate(out.metadata):\n",
" print('{}: {}'.format(i, m))"
"print(out.metadata[1])"
]
},
{
@ -66,7 +79,27 @@
"metadata": {},
"outputs": [],
"source": [
"load.files"
"' > '.join(filter(None, out.metadata[0].desc[3]))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"for x in out.metadata[0].desc:\n",
" print (x)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"for i, m in enumerate(out.metadata):\n",
" print('{}: {}'.format(i, m))"
]
},
{

27
ld2dap/AttributeProfiles.py
View File

@ -43,6 +43,13 @@ class AttributeProfiles(Filter):
att_offset[att] = len(values) * 2 + 1 if values is not None else 0
return att_offset
def _process_len(self):
att_len = dict()
for att in ['area', 'sd', 'moi']:
values = self.__getattribute__(att)
att_len[att] = len(values) if values is not None else 0
return att_len
def _process(self, data, metadata):
t = triskele.Triskele(data, verbose=False)
att_min = t.filter(tree='min-tree', area=self.area,
@ -58,23 +65,35 @@ class AttributeProfiles(Filter):
### Pre-process descriptions
att_desc = self._process_desc()
### Compute stack offsets
### Compute stack offsets and att length
att_len = self._process_len()
att_offset = self._process_offset()
stack_offset = sum(att_offset.values())
### Merge old and new descriptions
metadata_new = list()
### Re-order to create original APs
raster_list = list()
for stack in metadata:
if stack.end - stack.begin > 1:
raise NotImplementedError('Nested filtering not implemented yet')
do = dso = 0
for att in ['area', 'sd', 'moi']:
if att_offset[att] == 0:
continue
stack_new = Stack(stack_offset * stack.begin, att_offset[att],
al = att_len[att]
raster_list.append(att_min[:,:,do+al:do:-1])
raster_list.append(att_min[:,:,0])
raster_list.append(att_max[:,:,do+1:do+al+1])
do += al
stack_new = Stack(dso + stack_offset * stack.begin, att_offset[att],
stack.desc[0], stack.symb[0])
dso += att_offset[att]
for old_desc, new_desc in zip(stack_new.desc, att_desc[att]):
print('DESCRIPTION: {} > {}'.format(old_desc, new_desc))
old_desc.append(new_desc)
@ -82,9 +101,9 @@ class AttributeProfiles(Filter):
metadata_new.append(stack_new)
att = np.dstack((att_min, att_max))
data_new = np.dstack(raster_list)
return att, metadata_new
return data_new, metadata_new
if __name__ == '__main__':
area = [10, 100, 1000]

30
ld2dap/ShowFig.py
View File

@ -13,20 +13,32 @@ from ld2dap.core import Output
import matplotlib.pyplot as plt
class ShowFig(Output):
def __init__(self, fname, bbox_inches='tight', pad_inches=1):
def __init__(self, stack_id=0, bbox_inches='tight', pad_inches=1):
super().__init__(self.__class__.__name__)
self.fname = fname
self.bbox_inches = bbox_inches
self.pad_inches = pad_inches
self.stack_id = stack_id
def _process(self, data, metadata):
if self.stack_id == 'all':
for stack in metadata:
self._showfig(data, stack)
else:
stack = metadata[self.stack_id]
self._showfig(data, stack)
def _showfig(self, data, stack):
fig_count = stack.end - stack.begin
im_size = 2
fig = plt.figure(figsize=(16*im_size,3*im_size))
f1 = fig.add_subplot(111)
img = f1.imshow(data[:,:,-1])
plt.colorbar(img)
if metadata is not None:
print (metadata[0].desc)
f1.set_title(' > '.join(metadata[0].desc[-1]))
fig = plt.figure(figsize=(16*im_size,3*im_size*fig_count))
for i, di in enumerate(range(stack.begin, stack.end)):
f1 = fig.add_subplot(fig_count, 1, i + 1)
img = f1.imshow(data[:,:,di])
plt.colorbar(img)
f1.set_title(' > '.join(filter(None, stack.desc[i])))
plt.show()
plt.close(fig)