microsoft
/
poultry-cafos
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Код Задачи Пакеты Проекты Релизы Вики Активность

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Caleb Robinson 2022-07-13 17:45:14 +00:00
Родитель ee89f99b91
Коммит 258823bbd6
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6
README.md
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@ -24,10 +24,10 @@ If you make use of this implementation or data in your own project, or you want
## Setup
First, run the following commands to create a conda environment, "poultry", with the necessary dependencies for running the scripts and notebooks in this repository:
First, run the following commands to create a conda environment, "cafo", with the necessary dependencies for running the scripts and notebooks in this repository:
```bash
conda env create -f environment.yml
conda activate poultry
conda activate cafo
```
Next, follow the instructions in the following sub-sections to set up the different datasets.
@ -53,7 +53,7 @@ mv naip_blob_list.txt data/
Download the `Delmarva_PL_House_Final.zip` file from the Soroka and Duren 2020 *Poultry barn* dataset from [here](https://www.sciencebase.gov/catalog/item/5e0a3fcde4b0b207aa0d794e). From the unzipped directory run:
```
conda activate poultry
conda activate cafo
ogr2ogr -of GeoJSON -t_srs epsg:4326 Delmarva_PL_House_Final2_epsg4326.geojson Delmarva_PL_House_Final2.shp
ogr2ogr -of GeoJSON -t_srs epsg:32618 Delmarva_PL_House_Final2_epsg32618.geojson Delmarva_PL_House_Final2.shp
ogr2ogr -of GeoJSON -t_srs epsg:26918 Delmarva_PL_House_Final2_epsg26918.geojson Delmarva_PL_House_Final2.shp

6
cafo/data/StreamingDatasets.py
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@ -168,6 +168,12 @@ class StreamingGeospatialDataset(IterableDataset):
img, labels = self.sample_transform(img, labels)
if img.shape[0] != 4 or img.shape[1] != 256 or img.shape[2] != 256 or labels.shape[0] != 256 or labels.shape[1] != 256:
#img = torch.zeros(4,256,256).double()
#labels = torch.zeros(256,256).long()
print("Error", img.shape, labels.shape, img_fn, x, y)
continue
# Note, that img should be a torch "Double" type (i.e. a np.float32)
# and labels should be a torch "Long" type (i.e. np.int64)
yield img, labels

28
cafo/models.py
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@ -61,6 +61,34 @@ def get_unet_large():
classes=2,
)
def get_deeplab():
return smp.DeepLabV3Plus(
encoder_name="resnet18",
in_channels=4,
classes=2,
)
def get_unetplusplus():
return smp.UnetPlusPlus(
encoder_name="resnet18",
in_channels=4,
classes=2,
)
def get_manet():
return smp.MAnet(
encoder_name="resnet18",
in_channels=4,
classes=2,
)
def get_unet2():
return smp.Unet(
encoder_name="resnet18",
in_channels=4,
classes=2,
)
def get_fcn():
return FCN(num_input_channels=4, num_output_classes=2, num_filters=64)

17
cafo/utils.py
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@ -22,7 +22,7 @@ RASTERIO_BEST_PRACTICES = dict(
VSI_CURL_CACHE_SIZE="200000000",
)
NAIP_BLOB_ROOT = "https://naipblobs.blob.core.windows.net/naip"
NAIP_BLOB_ROOT = "https://naipeuwest.blob.core.windows.net/naip"
LOGGER = logging.getLogger("main")
@ -85,7 +85,7 @@ def fit(model, device, data_loader, num_batches, optimizer, criterion, epoch, me
losses = []
tic = time.time()
for batch_idx, (data, targets) in enumerate(data_loader):
if batch_idx % 10 == 0:
if batch_idx % 100 == 0:
elapsed_time = time.time() - tic
remaining_time = (
(elapsed_time / (batch_idx + 1)) * num_batches
@ -101,11 +101,14 @@ def fit(model, device, data_loader, num_batches, optimizer, criterion, epoch, me
targets = targets.to(device)
optimizer.zero_grad()
outputs = model(data)
loss = criterion(outputs, targets)
losses.append(loss.item())
loss.backward()
optimizer.step()
try:
outputs = model(data)
loss = criterion(outputs, targets)
losses.append(loss.item())
loss.backward()
optimizer.step()
except ValueError as e:
print(e, data.shape, targets.shape)
avg_loss = np.mean(losses)

2
environment.yml
Просмотреть файл

@ -12,7 +12,7 @@ dependencies:
- pandas
- pip
- python
- pytorch
- pytorch-gpu
- rasterio
- rtree
- scikit-image

11
inference.py
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@ -52,7 +52,10 @@ parser.add_argument(
)
parser.add_argument(
"--model", default="unet", choices=("unet", "fcn"), help="Model to use"
"--model",
default="unet",
choices=("unet", "manet", "unet++", "deeplabv3+"),
help="Model to use",
)
parser.add_argument(
@ -96,8 +99,12 @@ def main():
if args.model == "unet":
model = models.get_unet()
elif args.model == "fcn":
elif args.model == "unet++":
model = models.get_fcn()
elif args.model == "manet":
model = models.get_manet()
elif args.model == "deeplabv3+":
model = models.get_deeplab()
else:
raise ValueError("Invalid model")
model.load_state_dict(

12
inference_and_evaluate.py
Просмотреть файл

@ -57,9 +57,11 @@ parser.add_argument(
action="store_true",
help="Flag for overwriting `output_fn` if that directory already exists",
)
parser.add_argument(
"--model", default="unet", choices=("unet", "fcn"), help="Model to use"
"--model",
default="unet",
choices=("unet", "manet", "unet++", "deeplabv3+"),
help="Model to use",
)
args = parser.parse_args()
@ -101,8 +103,12 @@ def main():
if args.model == "unet":
model = models.get_unet()
elif args.model == "fcn":
elif args.model == "unet++":
model = models.get_fcn()
elif args.model == "manet":
model = models.get_manet()
elif args.model == "deeplabv3+":
model = models.get_deeplab()
else:
raise ValueError("Invalid model")
model.load_state_dict(torch.load(args.model_fn)["model_checkpoint"])

20
notebooks/Data preparation - Generate Chesapeake Bay county GeoJSON.ipynb
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@ -25,16 +25,16 @@
"name": "stdout",
"output_type": "stream",
"text": [
"--2021-08-04 22:51:00-- https://www2.census.gov/geo/tiger/GENZ2018/shp/cb_2018_us_county_5m.zip\n",
"Resolving www2.census.gov (www2.census.gov)... 23.47.20.127, 2600:1408:2000:1bc::208c, 2600:1408:2000:1b2::208c\n",
"Connecting to www2.census.gov (www2.census.gov)|23.47.20.127|:443... connected.\n",
"--2022-05-11 19:16:34-- https://www2.census.gov/geo/tiger/GENZ2018/shp/cb_2018_us_county_5m.zip\n",
"Resolving www2.census.gov (www2.census.gov)... 23.1.205.135, 2600:1400:11:18b::208c, 2600:1400:11:199::208c\n",
"Connecting to www2.census.gov (www2.census.gov)|23.1.205.135|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: unspecified [application/zip]\n",
"Saving to: ‘cb_2018_us_county_5m.zip’\n",
"\n",
"cb_2018_us_county_5 [ <=> ] 2.65M --.-KB/s in 0.04s \n",
"cb_2018_us_county_5 [ <=> ] 2.65M --.-KB/s in 0.08s \n",
"\n",
"2021-08-04 22:51:00 (64.8 MB/s) - ‘cb_2018_us_county_5m.zip’ saved [2781997]\n",
"2022-05-11 19:16:35 (33.9 MB/s) - ‘cb_2018_us_county_5m.zip’ saved [2781997]\n",
"\n",
"Archive: cb_2018_us_county_5m.zip\n",
" inflating: cb_2018_us_county_5m.shp.ea.iso.xml \n",
@ -120,6 +120,14 @@
"source": [
"!rm cb_2018_us_county_5m.*"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "90616b09",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
@ -138,7 +146,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.7"
"version": "3.10.4"
}
},
"nbformat": 4,

6
notebooks/Data preparation - Parse NAIP file list.ipynb
Просмотреть файл

@ -34,7 +34,7 @@
"with open(\"../data/naip_blob_list.txt\") as f:\n",
" lines = f.read().strip().split()\n",
" urls = [\n",
" \"https://naipblobs.blob.core.windows.net/naip/\" + line\n",
" \"https://naipeuwest.blob.core.windows.net/naip/\" + line\n",
" for line in lines\n",
" if line.endswith(\".tif\")\n",
" ]"
@ -249,7 +249,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 16,
"id": "medium-baltimore",
"metadata": {},
"outputs": [],
@ -284,7 +284,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.7"
"version": "3.10.4"
}
},
"nbformat": 4,

117
results/train-augment_deeplabv3+_0.05_0.01_rotation.csv Normal file
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@ -0,0 +1,117 @@
image_fn,label_fn,tp,fp,fn,tn,iou,recall,precision
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https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/37075/m_3707502_sw_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/37075/m_3707502_sw_18_1_20170611.tif,0,0,0,47045020,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/37075/m_3707503_ne_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/37075/m_3707503_ne_18_1_20170611.tif,26238,7824,2393,46797617,0.7197366616376354,0.9164192658307428,0.7703012154306852
https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/37075/m_3707503_nw_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/37075/m_3707503_nw_18_1_20170611.tif,0,14664,0,46902016,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/37075/m_3707504_ne_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/37075/m_3707504_ne_18_1_20170611.tif,92565,14353,8776,46590290,0.800084706207755,0.9134012887182877,0.8657569352213846
https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/37075/m_3707504_nw_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/37075/m_3707504_nw_18_1_20170611.tif,81795,11999,7226,46696068,0.8096911502672738,0.9188281416744364,0.8720707081476428
https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/37076/m_3707608_ne_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/37076/m_3707608_ne_18_1_20170611.tif,0,0,0,47173504,nan,nan,nan
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https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/38075/m_3807557_sw_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/38075/m_3807557_sw_18_1_20170611.tif,0,0,0,47082112,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/md/2017/md_100cm_2017/38075/m_3807558_se_18_1_20170611.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/md/2017/md_100cm_2017/38075/m_3807558_se_18_1_20170611.tif,64257,9238,5648,46791913,0.8119100868048975,0.9192046348615979,0.8743043744472413
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_se_18_1_20160626.tif,0,2520,0,47035492,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_sw_18_1_20160626.tif,0,954,0,47099814,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_ne_18_1_20160626.tif,0,0,0,46888485,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_nw_18_1_20160626.tif,0,1159,0,46943801,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_se_18_1_20160626.tif,0,0,0,46926390,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_sw_18_1_20160626.tif,0,1271,0,46974025,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_ne_18_1_20160626.tif,0,0,0,46777024,nan,nan,nan
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_se_18_1_20160626.tif,0,0,0,46807320,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_sw_18_1_20160626.tif,0,0,0,46863745,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707541_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707541_ne_18_1_20160626.tif,7074,4718,559,47063601,0.5727471459800826,0.9267653609327918,0.5998982360922659
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707542_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707542_ne_18_1_20160626.tif,0,0,0,46956714,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707542_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707542_nw_18_1_20160626.tif,0,628,0,47012588,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707543_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707543_nw_18_1_20160626.tif,0,0,0,46901630,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707608_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707608_ne_18_1_20160626.tif,0,1222,0,46850906,0.0,nan,0.0
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707616_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707616_ne_18_1_20160626.tif,0,0,0,46926669,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707648_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707648_ne_18_1_20160626.tif,0,0,0,47193948,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807560_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807560_se_18_1_20160626.tif,268279,28793,29298,46029072,0.8220087630603303,0.9015448102507923,0.9030773684493995
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807562_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807562_se_18_1_20160626.tif,0,0,0,46120064,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807563_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807563_sw_18_1_20160626.tif,0,21,0,46063977,0.0,nan,0.0
----
,Totals,2422878,463329,226452,5323632924,0.7783949350057299,0.9145248043845048,0.8394678552162059
Не удается отобразить этот файл, потому что он имеет неправильное количество полей в строке 116.

2411
results/train-augment_deeplabv3+_0.05_0.01_rotation.geojson Normal file
Просмотреть файл

Разница между файлами не показана из-за своего большого размера Загрузить разницу

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results/train-augment_manet_0.05_0.01_rotation.csv Normal file
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image_fn,label_fn,tp,fp,fn,tn,iou,recall,precision
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_se_18_1_20160626.tif,0,1302,0,47036710,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_sw_18_1_20160626.tif,0,0,0,47100768,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_ne_18_1_20160626.tif,0,0,0,46888485,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_nw_18_1_20160626.tif,0,19,0,46944941,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_se_18_1_20160626.tif,0,0,0,46926390,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_sw_18_1_20160626.tif,0,14,0,46975282,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_ne_18_1_20160626.tif,0,169,0,46776855,0.0,nan,0.0
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_sw_18_1_20160626.tif,0,0,0,46863745,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707541_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707541_ne_18_1_20160626.tif,7444,1792,189,47066527,0.7898143236074271,0.9752390934101925,0.8059766132524903
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707541_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707541_nw_18_1_20160626.tif,0,9742,0,47121394,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707542_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707542_ne_18_1_20160626.tif,0,0,0,46956714,nan,nan,nan
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707543_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707543_nw_18_1_20160626.tif,0,244,0,46901386,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707608_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707608_ne_18_1_20160626.tif,0,36,0,46852092,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707608_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707608_se_18_1_20160626.tif,0,0,0,46890108,nan,nan,nan
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707616_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707616_ne_18_1_20160626.tif,0,54,0,46926615,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707648_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707648_ne_18_1_20160626.tif,0,853,0,47193095,0.0,nan,0.0
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807563_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807563_sw_18_1_20160626.tif,0,0,0,46063998,nan,nan,nan
----
,Totals,2457099,405533,192231,5323690720,0.8043237945531436,0.9274416550599586,0.8583356156152799
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results/train-augment_manet_0.05_0.01_rotation.geojson Normal file
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Разница между файлами не показана из-за своего большого размера Загрузить разницу

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results/train-augment_unet++_0.05_0.01_rotation.csv Normal file
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image_fn,label_fn,tp,fp,fn,tn,iou,recall,precision
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707527_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707527_se_18_1_20160626.tif,0,4668883,0,42070271,0.0,nan,0.0
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https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707528_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707528_nw_18_1_20160626.tif,0,1005590,0,45648320,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707528_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707528_sw_18_1_20160626.tif,0,4603759,0,42080431,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_ne_18_1_20160626.tif,0,531386,0,46474880,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_nw_18_1_20160626.tif,0,834321,0,46228487,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_se_18_1_20160626.tif,0,150366,0,46887646,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707533_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707533_sw_18_1_20160626.tif,0,1747678,0,45353090,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_ne_18_1_20160626.tif,0,68282,0,46820203,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_nw_18_1_20160626.tif,0,38083,0,46906877,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_se_18_1_20160626.tif,0,5248,0,46921142,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707534_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707534_sw_18_1_20160626.tif,0,3137977,0,43837319,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_ne_18_1_20160626.tif,0,9430487,0,37346537,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_nw_18_1_20160626.tif,0,32395,0,46801042,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_se_18_1_20160626.tif,0,6735467,0,40071853,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707535_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707535_sw_18_1_20160626.tif,0,224047,0,46639698,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707541_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707541_ne_18_1_20160626.tif,5891,272891,1742,46795428,0.02099998574097047,0.7717804270928862,0.02113120646239714
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707541_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707541_nw_18_1_20160626.tif,0,968244,0,46162892,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707542_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707542_ne_18_1_20160626.tif,0,3581874,0,43374840,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707542_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707542_nw_18_1_20160626.tif,0,4951664,0,42061552,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37075/m_3707543_nw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37075/m_3707543_nw_18_1_20160626.tif,0,8530830,0,38370800,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707608_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707608_ne_18_1_20160626.tif,0,12716,0,46839412,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707608_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707608_se_18_1_20160626.tif,0,3312,0,46886796,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707616_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707616_ne_18_1_20160626.tif,0,8124,0,46918545,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/37076/m_3707648_ne_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/37076/m_3707648_ne_18_1_20160626.tif,0,95679,0,47098269,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807560_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807560_se_18_1_20160626.tif,175643,137121,121934,45920744,0.40405752959525926,0.5902438696539047,0.5615831745341535
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807561_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807561_se_18_1_20160626.tif,16962,31182,27045,46155655,0.22559150939632128,0.3854386802099666,0.3523180458624128
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807561_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807561_sw_18_1_20160626.tif,47499,27778,63898,46153948,0.34128974312915394,0.4263938885248256,0.6309895452794346
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807562_se_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807562_se_18_1_20160626.tif,0,272593,0,45847471,0.0,nan,0.0
https://landcover.blob.core.windows.net/poultry/naip/v002/va/2016/va_100cm_2016/38075/m_3807563_sw_18_1_20160626.tif,https://landcover.blob.core.windows.net/poultry/test-all/v002/va/2016/va_100cm_2016/38075/m_3807563_sw_18_1_20160626.tif,0,906277,0,45157721,0.0,nan,0.0
----
,Totals,1186401,87123160,1462929,5236973093,0.013215641005390404,0.4478117108853937,0.01343457023866306
Не удается отобразить этот файл, потому что он имеет неправильное количество полей в строке 116.

15
run_ablations.sh Normal file
Просмотреть файл

@ -0,0 +1,15 @@
python train.py --gpu 0 --num_dataloader_workers 12 --num_epochs 200 --batch_size 32 --training_set train-augment --model unet++ --negative_sample_probability 0.05 --lr 0.01 --save_most_recent --rotation_augmentation --output_dir output/train-single_unet++_0.05_0.01_rotation
python train.py --gpu 1 --num_dataloader_workers 12 --num_epochs 200 --batch_size 32 --training_set train-augment --model deeplabv3+ --negative_sample_probability 0.05 --lr 0.01 --save_most_recent --rotation_augmentation --output_dir output/train-single_deeplabv3+_0.05_0.01_rotation
python train.py --gpu 2 --num_dataloader_workers 12 --num_epochs 200 --batch_size 32 --training_set train-augment --model manet --negative_sample_probability 0.05 --lr 0.01 --save_most_recent --rotation_augmentation --output_dir output/train-single_manet_0.05_0.01_rotation
python inference_and_evaluate.py --gpu 3 --input_fn data/splits/test-single.csv --model_fn output/train-single_unet++_0.05_0.01_rotation/best_checkpoint.pt --output_fn results/train-augment_unet++_0.05_0.01_rotation.csv --model unet++
python inference_and_evaluate.py --gpu 3 --input_fn data/splits/test-single.csv --model_fn output/train-single_deeplabv3+_0.5_0.01_rotation_run2/best_checkpoint.pt --output_fn results/train-augment_deeplabv3+_0.05_0.01_rotation.csv --model deeplabv3+
python inference_and_evaluate.py --gpu 3 --input_fn data/splits/test-single.csv --model_fn output/train-single_manet_0.05_0.01_rotation/best_checkpoint.pt --output_fn results/train-augment_manet_0.05_0.01_rotation.csv --model manet
python inference.py --input_fn data/splits/test-single.csv --model_fn output/train-single_deeplabv3+_0.5_0.01_rotation_run2/best_checkpoint.pt --output_dir results/train-augment_deeplabv3+_0.05_0.01_rotation/ --gpu 0 --model deeplabv3+
python inference.py --input_fn data/splits/test-single.csv --model_fn output/train-single_manet_0.5_0.01_rotation/best_checkpoint.pt --output_dir results/train-augment_manet_0.05_0.01_rotation/ --gpu 1 --model manet
python postprocess.py --input_fn data/splits/test-single.csv --output_fn results/train-augment_deeplabv3+_0.05_0.01_rotation.geojson --input_dir results/train-augment_deeplabv3+_0.05_0.01_rotation/
python postprocess.py --input_fn data/splits/test-single.csv --output_fn results/train-augment_manet_0.05_0.01_rotation.geojson --input_dir results/train-augment_manet_0.05_0.01_rotation/

34
train.py
Просмотреть файл

@ -116,7 +116,7 @@ parser.add_argument(
parser.add_argument(
"--model",
default="unet",
choices=("unet", "unet-large", "fcn"),
choices=("unet", "manet", "unet++", "deeplabv3+"),
help="Model to use",
)
parser.add_argument(
@ -146,7 +146,6 @@ def joint_transform(img, labels):
rotate_amount = np.random.randint(0, 360)
img = rotate(img, rotate_amount)
labels = rotate(labels, rotate_amount, order=0)
labels = (labels * 255).astype(np.uint8)
img = img[
CROP_POINT : CROP_POINT + CHIP_SIZE, CROP_POINT : CROP_POINT + CHIP_SIZE
@ -157,6 +156,7 @@ def joint_transform(img, labels):
else:
img = img / 255.0
img = img[
CROP_POINT : CROP_POINT + CHIP_SIZE, CROP_POINT : CROP_POINT + CHIP_SIZE
]
@ -348,18 +348,18 @@ def main():
# Load input data
validation_image_fns = [
"naip/v002/de/2011/de_100cm_2011/38075/m_3807505_ne_18_1_20110602.tif",
"naip/v002/de/2013/de_100cm_2013/38075/m_3807505_ne_18_1_20130915.tif",
"naip/v002/de/2015/de_100cm_2015/38075/m_3807505_ne_18_1_20150629.tif",
"naip/v002/de/2017/de_100cm_2017/38075/m_3807505_ne_18_1_20170720.tif",
"naip/v002/de/2018/de_060cm_2018/38075/m_3807505_ne_18_060_20180827.tif",
"https://landcover.blob.core.windows.net/poultry/naip/v002/de/2011/de_100cm_2011/38075/m_3807505_ne_18_1_20110602.tif",
"https://landcover.blob.core.windows.net/poultry/naip/v002/de/2013/de_100cm_2013/38075/m_3807505_ne_18_1_20130915.tif",
"https://landcover.blob.core.windows.net/poultry/naip/v002/de/2015/de_100cm_2015/38075/m_3807505_ne_18_1_20150629.tif",
"https://landcover.blob.core.windows.net/poultry/naip/v002/de/2017/de_100cm_2017/38075/m_3807505_ne_18_1_20170720.tif",
"https://landcover.blob.core.windows.net/poultry/naip/v002/de/2018/de_060cm_2018/38075/m_3807505_ne_18_060_20180827.tif",
]
validation_label_fns = [
"train-augment/v002/de/2011/de_100cm_2011/38075/m_3807505_ne_18_1_20110602.tif",
"train-augment/v002/de/2013/de_100cm_2013/38075/m_3807505_ne_18_1_20130915.tif",
"train-augment/v002/de/2015/de_100cm_2015/38075/m_3807505_ne_18_1_20150629.tif",
"train-augment/v002/de/2017/de_100cm_2017/38075/m_3807505_ne_18_1_20170720.tif",
"train-augment/v002/de/2018/de_060cm_2018/38075/m_3807505_ne_18_060_20180827.tif",
"https://landcover.blob.core.windows.net/poultry/train-augment/v002/de/2011/de_100cm_2011/38075/m_3807505_ne_18_1_20110602.tif",
"https://landcover.blob.core.windows.net/poultry/train-augment/v002/de/2013/de_100cm_2013/38075/m_3807505_ne_18_1_20130915.tif",
"https://landcover.blob.core.windows.net/poultry/train-augment/v002/de/2015/de_100cm_2015/38075/m_3807505_ne_18_1_20150629.tif",
"https://landcover.blob.core.windows.net/poultry/train-augment/v002/de/2017/de_100cm_2017/38075/m_3807505_ne_18_1_20170720.tif",
"https://landcover.blob.core.windows.net/poultry/train-augment/v002/de/2018/de_060cm_2018/38075/m_3807505_ne_18_060_20180827.tif",
]
if args.training_set == "train-all":
@ -407,7 +407,7 @@ def main():
train_dataset,
batch_size=args.batch_size,
num_workers=NUM_WORKERS,
pin_memory=True,
pin_memory=False,
)
num_training_batches_per_epoch = int(
@ -422,10 +422,12 @@ def main():
# Setup training
if args.model == "unet":
model = models.get_unet()
elif args.model == "fcn":
elif args.model == "unet++":
model = models.get_fcn()
elif args.model == "unet-large":
model = models.get_unet_large()
elif args.model == "manet":
model = models.get_manet()
elif args.model == "deeplabv3+":
model = models.get_deeplab()
else:
raise ValueError("Invalid model")