import io import json import os import sys import argparse import re from loguru import logger import tensorflow as tf from lib.dataset.batched_iterator import batched_iterator from lib.vis.segmentation_plot import segmentation_plot from lib.io.handle_open import handle_open from lib.ai.RainfallWaterSegmenter import RainfallWaterSegmenter from lib.dataset.dataset_segmenter import dataset_predict from lib.io.find_paramsjson import find_paramsjson from lib.io.readfile import readfile from lib.vis.segmentation_plot import segmentation_plot MODE_JSONL = 1 MODE_PNG = 2 def parse_args(): parser = argparse.ArgumentParser(description="Output water depth image segmentation maps using a given pretrained image segmentation model.") # parser.add_argument("--config", "-c", help="Filepath to the TOML config file to load.", required=True) parser.add_argument("--input", "-i", help="Path to input directory containing the .tfrecord(.gz) files to predict for. If a single file is passed instead, then only that file will be converted.", required=True) parser.add_argument("--output", "-o", help="Path to output file to write output to. If the file extension .png is used instead of .jsonl.gz, then an image is written instead (+d is replaced with the item index).") parser.add_argument("--records-per-file", help="Optional, only valid with the .jsonl.gz file extension. If specified, this limits the number of records written to each file. When using this option, you MUST have the string '+d' (without quotes) somewhere in your output filepath.", type=int) parser.add_argument("--checkpoint", "-c", help="Checkpoint file to load model weights from.", required=True) parser.add_argument("--params", "-p", help="Optional. The file containing the model hyperparameters (usually called 'params.json'). If not specified, it's location will be determined automatically.") parser.add_argument("--reads-multiplier", help="Optional. The multiplier for the number of files we should read from at once. Defaults to 0. When using this start with 1.5, which means read ceil(NUMBER_OF_CORES * 1.5). Set to a higher number of systems with high read latency to avoid starving the GPU of data. SETTING THIS WILL SCRAMBLE THE ORDER OF THE DATASET.") parser.add_argument("--model-code", help="A description of the model used to predict the data. Will be inserted in the title of png plots.") parser.add_argument("--log", help="Optional. If specified when the file extension is .jsonl[.gz], then this chooses what is logged. Specify a comma separated list of values. Possible values: rainfall_actual, water_actual, water_predict. Default: rainfall_actual,water_actual,water_predict.") return parser def run(args): # Note that we do NOT check to see if the checkpoint file exists, because Tensorflow/Keras requires that we pass the stem instead of the actual index file..... :-/ if (not hasattr(args, "params")) or args.params == None: args.params = find_paramsjson(args.checkpoint) if args.params == None: logger.error("Error: Failed to find params.json. Please ensure it's either in the same directory as the checkpoint or 1 level above") return if (not hasattr(args, "read_multiplier")) or args.read_multiplier == None: args.read_multiplier = 0 if (not hasattr(args, "records_per_file")) or args.records_per_file == None: args.records_per_file = 0 # 0 = unlimited if (not hasattr(args, "output")) or args.output == None: args.output = "-" if (not hasattr(args, "model_code")) or args.model_code == None: args.model_code = "" if (not hasattr(args, "log")) or args.log == None: args.log = "rainfall_actual,water_actual,water_predict" args.log = args.log.strip().split(",") if not os.path.exists(args.params): raise Exception(f"Error: The specified filepath params.json hyperparameters ('{args.params}) does not exist.") if not os.path.exists(args.checkpoint): raise Exception(f"Error: The specified filepath to the checkpoint to load ('{args.checkpoint}) does not exist.") if args.records_per_file > 0 and args.output.endswith(".jsonl.gz"): dirpath_output=os.path.dirname(args.output) if not os.path.exists(dirpath_output): os.mkdir(dirpath_output) model_params = json.loads(readfile(args.params)) ai = RainfallWaterSegmenter.from_checkpoint(args.checkpoint, **model_params) sys.stderr.write(f"\n\n>>> This is TensorFlow {tf.__version__}\n\n\n") # Note that if using a directory of input files, the output order is NOT GUARANTEED TO BE THE SAME. In fact, it probably won't be. dataset = dataset_predict( dirpath_input=args.input, parallel_reads_multiplier=args.read_multiplier ) # for items in dataset_train.repeat(10): # print("ITEMS", len(items)) # print("LEFT", [ item.shape for item in items[0] ]) # print("ITEMS DONE") # exit(0) output_mode = MODE_PNG if args.output.endswith(".png") else MODE_JSONL logger.info("Output mode is "+("PNG" if output_mode == MODE_PNG else "JSONL")) logger.info(f"Records per file: {args.records_per_file}") if output_mode == MODE_JSONL: do_jsonl(args, ai, dataset, model_params) else: do_png(args, ai, dataset, model_params) sys.stderr.write(">>> Complete\n") def do_png(args, ai, dataset, model_params): if not os.path.exists(os.path.dirname(args.output)): os.mkdir(os.path.dirname(args.output)) i = 0 gen = batched_iterator(dataset, tensors_in_item=2, batch_size=model_params["batch_size"]) for item in gen: rainfall, water = item water_predict_batch = ai.embed(rainfall) water = tf.unstack(water, axis=0) i_batch = 0 for water_predict in water_predict_batch: # [ width, height, softmax_probabilities ] → [ batch, width, height ] water_predict = tf.math.argmax(water_predict, axis=-1) # [ width, height ] water_actual = tf.squeeze(water[i_batch]) segmentation_plot( water_actual, water_predict, args.model_code, args.output.replace("+d", str(i)) ) i_batch += 1 i += 1 if i % 100 == 0: sys.stderr.write(f"Processed {i} items\r") def do_jsonl(args, ai, dataset, model_params): write_mode = "wt" if args.output.endswith(".gz") else "w" handle = sys.stdout filepath_metadata = None if args.output != "-": handle = handle_open( args.output if args.records_per_file <= 0 else args.output.replace("+d", str(0)), write_mode ) filepath_metadata = os.path.join(os.path.dirname(args.output), "metadata.json") logger.info(f"filepath_output: {args.output}") logger.info(f"filepath_params: {filepath_metadata}") i = 0 i_file = i files_done = 0 for batch in batched_iterator(dataset, tensors_in_item=2, batch_size=model_params["batch_size"]): rainfall_actual_batch, water_actual_batch = batch water_predict_batch = ai.embed(rainfall_actual_batch) water_actual_batch = tf.unstack(water_actual_batch, axis=0) rainfall_actual_batch = tf.unstack(rainfall_actual_batch, axis=0) i_batch = 0 for water_predict in water_predict_batch: # [ width, height, softmax_probabilities ] → [ batch, width, height ] # water_predict = tf.math.argmax(water_predict, axis=-1) # [ width, height ] water_actual = tf.squeeze(water_actual_batch[i_batch]) if args.records_per_file > 0 and i_file > args.records_per_file: files_done += 1 i_file = 0 handle.close() logger.info(f"PROGRESS:file {files_done}") handle = handle_open(args.output.replace("+d", str(files_done+1)), write_mode) item_obj = {} if "rainfall_actual" in args.log: item_obj["rainfall_actual"] = rainfall_actual_batch[i_batch].numpy().tolist() if "water_actual" in args.log: item_obj["water_actual"] = water_actual.numpy().tolist() if "water_predict" in args.log: item_obj["water_predict"] = water_predict.numpy().tolist() handle.write(json.dumps(item_obj, separators=(',', ':'))+"\n") # Ref https://stackoverflow.com/a/64710892/1460422 if i == 0 or i % 100 == 0: sys.stderr.write(f"[pretrain:predict] STEP {i}\r") i_batch += 1 i += 1 i_file += 1 handle.close()