diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 621c8bd..2dece09 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,12 +12,9 @@ repos: hooks: - id: poetry-check - id: poetry-lock - - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: v0.0.265 + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.4.2 hooks: - id: ruff args: [ --fix ] - - repo: https://github.com/psf/black - rev: 23.3.0 - hooks: - - id: black + - id: ruff-format diff --git a/docs/about.md b/docs/about.md index 7eb9b30..754039f 100644 --- a/docs/about.md +++ b/docs/about.md @@ -87,18 +87,21 @@ flowchart TD **Kelp (species)** -| Split | Scenes | Tiles | Pixels~macro~ | Pixels~nereo~ | Pixels~total~ | Area (km^2^) | Res~max~ (m) | Res~min~ (m) | Res~$\mu$~ (m) | Res~$\sigma$~ (m) | -|:------|-------:|-------:|--------------:|--------------:|--------------:|-------------:|-------------:|-------------:|---------------:|------------------:| -| Train | 17 | 336740 | 605462674 | 1158650042 | 88008624978 | 4034.11 | 0.1040 | 0.0230 | 0.0488 | 0.0266 | -| Val. | 4 | 15805 | 127410722 | 20244320 | 4110229732 | 123.91 | 0.0420 | 0.0230 | 0.0296 | 0.0085 | -| Test | 6 | 46304 | 143277498 | 176569508 | 12046802177 | 409.72 | 0.0680 | 0.0230 | 0.0385 | 0.0161 | -| *Sum* | 27 | 398849 | 876150894 | 1355463870 | 104165656887 | 4567.75 | | | | | +| Split | Scenes | Tiles | Pixels~macro~ | Pixels~nereo~ | Pixels~total~ | Area (km^2^) | Res~max~ (m) | Res~min~ (m) | Res~$\mu$~ (m) | Res~$\sigma$~ (m) | +|:-----------|-------:|-------:|--------------:|--------------:|--------------:|-------------:|-------------:|-------------:|---------------:|------------------:| +| Train | 17 | 336740 | 605462674 | 1158650042 | 88008624978 | 4034.11 | 0.1040 | 0.0230 | 0.0488 | 0.0266 | +| Validation | 4 | 15805 | 127410722 | 20244320 | 4110229732 | 123.91 | 0.0420 | 0.0230 | 0.0296 | 0.0085 | +| Test | 6 | 46304 | 143277498 | 176569508 | 12046802177 | 409.72 | 0.0680 | 0.0230 | 0.0385 | 0.0161 | +| *Sum* | 27 | 398849 | 876150894 | 1355463870 | 104165656887 | 4567.75 | | | | | **Mussels (presence/absence)** -!!! todo - - The mussel model is a work in progress. This section will be available in the future. +| Split | Scenes | Tiles | Pixels~mussels~ | Pixels~total~ | Area (km^2^) | Res~max~ (m) | Res~min~ (m) | Res~$\mu$~ (m) | Res~$\sigma$~ (m) | +|:-----------|-------:|------:|----------------:|--------------:|-------------:|-------------:|-------------:|---------------:|------------------:| +| Train | 39 | 4834 | 933287123 | 5068816384 | 23.8147 | 0.027 | 0.00231 | 0.0082244 | 0.00492054 | +| Validation | 8 | 1277 | 223598444 | 1339031552 | 5.74255 | 0.00518591 | 0.00330667 | 0.00421985 | 0.000545617 | +| Test | 8 | 1110 | 175226412 | 1163919360 | 4.64052 | 0.00578278 | 0.003671 | 0.00435929 | 0.000665025 | +| *Sum* | 55 | 7221 | 1332111979 | 7571767296 | 34.197799 | 0.037969 | 0.009288 | 0.016804 | 0.006131 | ## Model Training @@ -333,22 +336,26 @@ $$ **Mussels (presence/absence)** -!!! todo +=== "Test split" - The mussel model is a work in progress. This section will be updated in the future. + | Class | IoU | Precision | Recall | Accuracy | + |:------------|-------:|----------:|-------:|---------:| + | Mussels | 0.7360 | 0.8314 | 0.8262 | - | + | Not Mussels | 0.9824 | 0.9880 | 0.9942 | - | + | *Mean* | 0.8592 | 0.9097 | 0.9102 | 0.9847 | === "Validation split" | Class | IoU | Precision | Recall | Accuracy | |:------------|-------:|----------:|-------:|---------:| - | Mussels | 0.7684 | 0.8594 | 0.8777 | - | - | Not Mussels | 0.9805 | 0.9917 | 0.9886 | - | - | *Mean* | 0.8745 | 0.9721 | 0.9721 | 0.9331 | + | Mussels | 0.7863 | 0.9232 | 0.8433 | - | + | Not Mussels | 0.9822 | 0.9887 | 0.9933 | - | + | *Mean* | 0.8843 | 0.9560 | 0.9183 | 0.9846 | === "Train split" | Class | IoU | Precision | Recall | Accuracy | |:------------|-------:|----------:|-------:|---------:| - | Mussels | 0.8344 | 0.8636 | 0.9595 | - | - | Not Mussels | 0.9770 | 0.9892 | 0.9874 | - | - | *Mean* | 0.9057 | 0.9264 | 0.9735 | 0.9062 | + | Mussels | 0.7499 | 0.8698 | 0.8425 | - | + | Not Mussels | 0.9783 | 0.9889 | 0.9891 | - | + | *Mean* | 0.8641 | 0.9294 | 0.9158 | 0.9806 | diff --git a/kelp_o_matic/geotiff_io/geotiff_reader.py b/kelp_o_matic/geotiff_io/geotiff_reader.py index 3294294..3bdf7ac 100644 --- a/kelp_o_matic/geotiff_io/geotiff_reader.py +++ b/kelp_o_matic/geotiff_io/geotiff_reader.py @@ -4,6 +4,7 @@ Date: 2021-02-22 Description: A Pytorch Dataset for geotiff images that dynamically crops the image. """ + import itertools from pathlib import Path from typing import List, Optional, Union diff --git a/kelp_o_matic/geotiff_io/geotiff_writer.py b/kelp_o_matic/geotiff_io/geotiff_writer.py index 13101f0..1fef559 100644 --- a/kelp_o_matic/geotiff_io/geotiff_writer.py +++ b/kelp_o_matic/geotiff_io/geotiff_writer.py @@ -4,6 +4,7 @@ Date: 2021-02-22 Description: A Pytorch Dataset for geotiff images that dynamically crops the image. """ + from pathlib import Path from typing import Union diff --git a/kelp_o_matic/hann.py b/kelp_o_matic/hann.py index a72a4a3..4c2334f 100644 --- a/kelp_o_matic/hann.py +++ b/kelp_o_matic/hann.py @@ -150,21 +150,21 @@ def step(self, new_logits: torch.Tensor, img_window: Window): logits_bd = logits_abcd[:, :, self.hws :] # write c0 - self.register[ - :, :, img_window.col_off : img_window.col_off + self.hws - ] = logits_c0 + self.register[:, :, img_window.col_off : img_window.col_off + self.hws] = ( + logits_c0 + ) # write bd col_off_bd = img_window.col_off + self.hws self.register[:, :, col_off_bd : col_off_bd + (self.ws - self.hws)] = logits_bd # Return the information-complete predictions - preds_win = Window( + logits_win = Window( col_off=img_window.col_off, row_off=img_window.row_off, height=min(self.hws, img_window.height), width=min(self.hws, img_window.width), ) - preds = logits_a[:, : img_window.height, : img_window.width].softmax(axis=0) + logits = logits_a[:, : img_window.height, : img_window.width] - return preds, preds_win + return logits, logits_win diff --git a/kelp_o_matic/models.py b/kelp_o_matic/models.py index f56f109..f8d99c7 100644 --- a/kelp_o_matic/models.py +++ b/kelp_o_matic/models.py @@ -12,6 +12,7 @@ class _Model(ABC): register_depth = 2 + all_black_val = 1 @staticmethod def transform(x: Union[np.ndarray, Image]) -> torch.Tensor: @@ -53,7 +54,7 @@ def shortcut(self, crop_size: int): logits = torch.zeros( (self.register_depth, crop_size, crop_size), device=self.device ) - logits[0] = 1 + logits[0] = self.all_black_val return logits @@ -97,10 +98,21 @@ class KelpRGBSpeciesSegmentationModel(_SpeciesSegmentationModel): class MusselRGBPresenceSegmentationModel(_Model): - torchscript_path = "LRASPP_MobileNetV3_mussel_presence_rgb_jit_miou=0.8745.pt" + register_depth = 1 + all_black_val = -1 + + torchscript_path = ( + "UNetPlusPlus_EfficientNetB4_mussel_presence_rgb_jit_dice=0.9269.pt" + ) + + def post_process(self, x: "torch.Tensor") -> "np.ndarray": + with torch.no_grad(): + label = (torch.sigmoid(x) > 0.5).to(torch.uint8)[0] + + return label.detach().cpu().numpy() -def _unet_efficientnet_b4_transform(x: Union[np.ndarray, Image]) -> torch.Tensor: +def _rgbi_kelp_transform(x: Union[np.ndarray, Image]) -> torch.Tensor: # to float x = f.to_tensor(x)[:4, :, :].to(torch.float) # min-max scale @@ -119,7 +131,7 @@ class KelpRGBIPresenceSegmentationModel(_Model): @staticmethod def transform(x: Union[np.ndarray, Image]) -> torch.Tensor: - return _unet_efficientnet_b4_transform(x) + return _rgbi_kelp_transform(x) class KelpRGBISpeciesSegmentationModel(_SpeciesSegmentationModel): @@ -130,4 +142,4 @@ class KelpRGBISpeciesSegmentationModel(_SpeciesSegmentationModel): @staticmethod def transform(x: Union[np.ndarray, Image]) -> torch.Tensor: - return _unet_efficientnet_b4_transform(x) + return _rgbi_kelp_transform(x) diff --git a/poetry.lock b/poetry.lock index 24cad32..6370fbd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -48,61 +48,15 @@ files = [ [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] -[[package]] -name = "black" -version = "23.12.1" -description = "The uncompromising code formatter." -optional = false -python-versions = ">=3.8" -files = [ - {file = "black-23.12.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e0aaf6041986767a5e0ce663c7a2f0e9eaf21e6ff87a5f95cbf3675bfd4c41d2"}, - {file = "black-23.12.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c88b3711d12905b74206227109272673edce0cb29f27e1385f33b0163c414bba"}, - 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