diff --git a/.gitignore b/.gitignore index 24ceb6e..5d027ff 100644 --- a/.gitignore +++ b/.gitignore @@ -25,6 +25,11 @@ wheels/ .installed.cfg *.egg +# Data/Predictions +fovs* +model* +predictions* + # OS generated files .DS_Store diff --git a/examples/download_and_train.py b/examples/download_and_train.py index ba2bd26..297facf 100644 --- a/examples/download_and_train.py +++ b/examples/download_and_train.py @@ -34,7 +34,7 @@ n_images_to_download = args.n_imgs # more images the better train_fraction = 0.75 -image_save_dir = "{}/".format(os.getcwd()) +image_save_dir = "{}".format(os.getcwd()) model_save_dir = "{}/model/".format(os.getcwd()) prefs_save_path = "{}/prefs.json".format(model_save_dir) @@ -82,10 +82,8 @@ df = pd.DataFrame(columns=["path_tiff", "channel_signal", "channel_target"]) df["path_tiff"] = image_target_paths -df["channel_signal"] = data_manifest["ChannelNumberBrightfield"] -df["channel_target"] = data_manifest[ - "ChannelNumber405" -] # this is the DNA channel for all FOVs +df["channel_signal"] = data_manifest["ChannelNumberBrightfield"].tolist() +df["channel_target"] = data_manifest["ChannelNumber405"].tolist() # this is the DNA channel for all FOVs n_train_images = int(n_images_to_download * train_fraction) df_train = df[:n_train_images]