Add LocalFeatures filter
This commit is contained in:
parent
10b3a75ee1
commit
be3c43849d
@ -77,7 +77,7 @@
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster_p = Path('../Data/phase1_rasters/Intensity_C3/UH17_GI3F051_TR.tif')\n",
|
||||
"raster_p = Path('../Data/phase1_rasters/DEM+B_C123/UH17_GEM051_TR.tif')\n",
|
||||
"raster = triskele.read(raster_p)\n",
|
||||
"DFC_filter(raster)"
|
||||
]
|
||||
@ -105,9 +105,11 @@
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"#area = np.array([25, 100, 500, 1e3, 5e3, 10e3, 50e3, 100e3, 150e3])\n",
|
||||
"area = [100, 1e3, 1e4, 1e5]\n",
|
||||
"area = [1e3, 1e6]\n",
|
||||
"moi = [.5, .7, .9]\n",
|
||||
"sd = [.1, .5, .9]\n",
|
||||
"moi = None\n",
|
||||
"sd = None\n",
|
||||
"\n",
|
||||
"t = triskele.Triskele(raster, verbose=False)\n",
|
||||
"attributes = t.filter(tree='tos-tree',\n",
|
||||
@ -147,7 +149,7 @@
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"a = attributes\n",
|
||||
"i = 3\n",
|
||||
"i = 1\n",
|
||||
"show(a[:,:,i].astype(np.float) - a[:,:,i+1])"
|
||||
]
|
||||
},
|
||||
@ -158,6 +160,15 @@
|
||||
"## Compute patches"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"patch_size = 5"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
@ -189,7 +200,7 @@
|
||||
" stack.append(offset)\n",
|
||||
" return np.stack(stack, axis=-1)\n",
|
||||
"\n",
|
||||
"offset_stack = create_patches(attributes, 5)\n",
|
||||
"offset_stack = create_patches(attributes, patch_size)\n",
|
||||
"offset_stack.shape"
|
||||
]
|
||||
},
|
||||
@ -263,6 +274,36 @@
|
||||
"stack_max = np.max(offset_stack, axis=-1)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"np.std.__name__"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"create_patches.__name__"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"for func in (np.mean, np.var):\n",
|
||||
" tmp = func(offset_stack, axis=-1)\n",
|
||||
" show(tmp[:,:,0])\n",
|
||||
" print(tmp.shape)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
@ -314,6 +355,159 @@
|
||||
" ]\n",
|
||||
"mshow(figs, ttls, 2, save='mstack2.png')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### TMP TRISLEK DBG"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"normal = triskele.read('../triskele/build/out/test-default.tif')\n",
|
||||
"sd = triskele.read('../triskele/build/out/test-sd.tif')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"normal.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"areas = np.loadtxt('../triskele/data/areaThresholds.txt')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"figs = [normal[:,:,0]]\n",
|
||||
"ttls = ['Origin']\n",
|
||||
"\n",
|
||||
"for area, i in zip(areas, range(1,normal.shape[2])):\n",
|
||||
" figs.append(normal[:,:,i])\n",
|
||||
" ttls.append('SDAP area {}'.format(area))\n",
|
||||
"\n",
|
||||
"mshow(figs, ttls, 2, '../Res/trkldbg_triskele_ap.png')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"figs = [sd[:,:,0]]\n",
|
||||
"ttls = ['Origin']\n",
|
||||
"\n",
|
||||
"for area, i in zip(areas, range(1,sd.shape[2])):\n",
|
||||
" figs.append(sd[:,:,i])\n",
|
||||
" ttls.append('Triskele LFSDAP (SD) area {}'.format(area))\n",
|
||||
"\n",
|
||||
"mshow(figs, ttls, 2, '../Res/trkldbg_triskele_sd.png')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"(normal == sd).all()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"offset_stack = create_patches(normal, 5)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"stack_std = np.std(offset_stack, axis=-1)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"figs = [stack_std[:,:,0]]\n",
|
||||
"ttls = ['Origin std 5x5']\n",
|
||||
"\n",
|
||||
"for area, i in zip(areas, range(1,sd.shape[2])):\n",
|
||||
" figs.append(stack_std[:,:,i])\n",
|
||||
" ttls.append('LD2DAPs LFSDAP std 5x5 area {}'.format(area))\n",
|
||||
"\n",
|
||||
"mshow(figs, ttls, 2, '../Res/trkldbg_ld2dap_sd.png')"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"figs = list()\n",
|
||||
"ttls = list()\n",
|
||||
"for d in range(stack_std.shape[-1]):\n",
|
||||
" if d == 0:\n",
|
||||
" ttls.append('Origin')\n",
|
||||
" else:\n",
|
||||
" ttls.append('STD 5x5 from area {}'.format(area[d-1]))\n",
|
||||
" figs.append(stack_std[:,:,d])\n",
|
||||
" \n",
|
||||
"mshow(figs, ttls, 2)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"assert True"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"assert False"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
|
||||
164
Notebooks/Node LFAPs.ipynb
Normal file
164
Notebooks/Node LFAPs.ipynb
Normal file
@ -0,0 +1,164 @@
|
||||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import sys\n",
|
||||
"from pathlib import Path\n",
|
||||
"import numpy as np\n",
|
||||
"import matplotlib.pyplot as plt\n",
|
||||
"import collections\n",
|
||||
"\n",
|
||||
"ld2dap_path = Path('../')\n",
|
||||
"sys.path.append(str(ld2dap_path.resolve()))\n",
|
||||
"import ld2dap\n",
|
||||
"from ld2dap.core import Filter"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"layers_files = [\n",
|
||||
" '../Data/phase1_rasters/DEM+B_C123/UH17_GEM051_TR.tif',\n",
|
||||
" '../Data/phase1_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif',\n",
|
||||
" '../Data/phase1_rasters/DEM_C123_TLI/UH17_GEG05_TR.tif',\n",
|
||||
" '../Data/phase1_rasters/DSM_C12/UH17c_GEF051_TR.tif',\n",
|
||||
" '../Data/phase1_rasters/Intensity_C1/UH17_GI1F051_TR.tif',\n",
|
||||
" '../Data/phase1_rasters/Intensity_C2/UH17_GI2F051_TR.tif',\n",
|
||||
" '../Data/phase1_rasters/Intensity_C3/UH17_GI3F051_TR.tif'\n",
|
||||
"]"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"# Node Streaming Local FeaturesAttribute Profiles\n",
|
||||
"\n",
|
||||
"We made some custom LFAPs in Python, but now Triskele comes with its owns in C++! Let's try it out then create a streaming node.\n",
|
||||
"\n",
|
||||
"## Triskele LFAPs"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import sys\n",
|
||||
"sys.path.append('../triskele/python/')\n",
|
||||
"import triskele"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"raster = triskele.read(layers_files[0])\n",
|
||||
"raster.shape"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"lfaps = triskele.Triskele(raster)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"results = lfaps.filter(area=[100, 1e4], feature='SD')\n",
|
||||
"results.shape, lfaps.process"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Streamin Node"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"import logging\n",
|
||||
"logger = logging.getLogger()\n",
|
||||
"logger.setLevel(logging.DEBUG)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"l = ld2dap.LoadTIFF(layers_files)\n",
|
||||
"t = ld2dap.Treshold(1e4)\n",
|
||||
"a = ld2dap.LocalFeatures([np.var, np.std, ])#, sd=[.4,.6,.8], moi=[.5,.9])\n",
|
||||
"d = ld2dap.ShowFig(stack_id='all', symb=False)\n",
|
||||
"o = ld2dap.RawOutput()\n",
|
||||
"\n",
|
||||
"o.input = a\n",
|
||||
"d.input = a\n",
|
||||
"a.input = t\n",
|
||||
"t.input = l\n",
|
||||
"\n",
|
||||
"d.run()"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"print(o.metadata[0])"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 2
|
||||
}
|
||||
94
ld2dap/LocalFeatures.py
Normal file
94
ld2dap/LocalFeatures.py
Normal file
@ -0,0 +1,94 @@
|
||||
#!/usr/bin/python
|
||||
# -*- coding: utf-8 -*-
|
||||
# \file LocalFeatures.py
|
||||
# \brief TODO
|
||||
# \author Florent Guiotte <florent.guiotte@gmail.com>
|
||||
# \version 0.1
|
||||
# \date 23 août 2018
|
||||
#
|
||||
# TODO details
|
||||
|
||||
from ld2dap.core import Filter, Stack
|
||||
import numpy as np
|
||||
|
||||
class LocalFeatures(Filter):
|
||||
def __init__(self, features=None, patch_size=3):
|
||||
super().__init__(self.__class__.__name__)
|
||||
self.features = features
|
||||
self.patch_size = patch_size
|
||||
|
||||
def _process(self, data, metadata):
|
||||
self.logger.info('Local Features Filtering')
|
||||
stacker = Stacker()
|
||||
|
||||
for stack in metadata:
|
||||
self.logger.debug('{}'.format(stack))
|
||||
|
||||
patches = create_patches(data[:,:,stack.begin:stack.end], self.patch_size)
|
||||
|
||||
for function in self.features:
|
||||
self.logger.debug('Features function {}'.format(function.__name__))
|
||||
features = function(patches, axis=-1)
|
||||
|
||||
stacker.auto_stack(features, stack,
|
||||
'Local Features {}'.format(function.__name__),
|
||||
'f^{{{}}}'.format(function.__name__))
|
||||
|
||||
return stacker.pack()
|
||||
|
||||
def create_patches(array, patch_size=3):
|
||||
amp = int((patch_size - 1 ) / 2)
|
||||
|
||||
stack = list()
|
||||
for i in range(-amp, amp+1):
|
||||
ai = i if i > 0 else None
|
||||
bi = i if i < 0 else None
|
||||
ci = -bi if bi is not None else None
|
||||
di = -ai if ai is not None else None
|
||||
|
||||
for j in range(-amp, amp+1):
|
||||
offset = np.zeros_like(array)
|
||||
#offset = np.empty(array.shape)
|
||||
aj = j if j > 0 else None
|
||||
bj = j if j < 0 else None
|
||||
cj = -bj if bj is not None else None
|
||||
dj = -aj if aj is not None else None
|
||||
offset[ai:bi, aj:bj] = array[ci:di, cj:dj]
|
||||
stack.append(offset)
|
||||
return np.stack(stack, axis=-1)
|
||||
|
||||
class Stacker:
|
||||
def __init__(self):
|
||||
self.offset = 0
|
||||
self.data_list = list()
|
||||
self.metadata_list = list()
|
||||
|
||||
def auto_stack(self, data, old_stack, desc_str, symb_str):
|
||||
if data.shape[-1] != (old_stack.end - old_stack.begin):
|
||||
raise ValueError("Mismatch between data shape and stack length")
|
||||
|
||||
new_desc = list()
|
||||
for d in old_stack.desc:
|
||||
new_desc.append(d.copy())
|
||||
new_desc[-1].append(desc_str)
|
||||
|
||||
new_symb = list()
|
||||
for s in old_stack.symb:
|
||||
new_symb.append([symb_str + '('])
|
||||
new_symb[-1].extend(s.copy())
|
||||
new_symb[-1].append(')')
|
||||
|
||||
self.stack(data, new_desc, new_symb)
|
||||
|
||||
def stack(self, data, desc, symb):
|
||||
size_new = data.shape[-1]
|
||||
stack_new = Stack(self.offset, size_new)
|
||||
self.offset += size_new
|
||||
stack_new.desc = desc
|
||||
stack_new.symb = symb
|
||||
self.data_list.append(data)
|
||||
self.metadata_list.append(stack_new)
|
||||
|
||||
def pack(self):
|
||||
return np.dstack(self.data_list), self.metadata_list
|
||||
|
||||
@ -20,6 +20,7 @@ class Treshold(Filter):
|
||||
|
||||
def _process(self, data, metadata):
|
||||
# TODO: UPGRADE STACK DEPENDANCE
|
||||
# TODO: Verify if the previous TODO is up to date
|
||||
# This filter each raster independently
|
||||
self.logger.info('Filtering')
|
||||
|
||||
|
||||
@ -10,6 +10,7 @@
|
||||
|
||||
from .AttributeProfiles import AttributeProfiles
|
||||
from .SelfDualAttributeProfiles import SelfDualAttributeProfiles
|
||||
from .LocalFeatures import LocalFeatures
|
||||
from .Treshold import Treshold
|
||||
from .LoadTIFF import LoadTIFF
|
||||
from .SaveFig import SaveFig
|
||||
|
||||
Loading…
Reference in New Issue
Block a user