Cleaner implementations of benchmark stuff

olmocr/bench/benchmark.py

@@ -4,9 +4,11 @@ This script runs olmocr bench.
 It will take as an argument a folder, and scan it for .jsonl files which contain the various rules and properties that we will check.
 It will then validate the JSON files to make sure they are all valid.
 Then, each other folder in there (besides /pdfs) represents a pipeline tool that we will evaluate.
-We will validate that each one of those contains a .md file corresponding to its parse for every .pdf in the /pdfs folder.
+We will validate that each one of those contains at least one .md file (or repeated generations, e.g. _1.md, _2.md, etc.)
+corresponding to its parse for every .pdf in the /pdfs folder.
 Then, we will read each one, and check if they pass against all the rules.
-If a rule fails, a short explanation is printed.
+If a rule fails on some of the repeats, a short explanation is printed.
+The final score is averaged over the repeated generations.
 """
 
 import argparse
@@ -44,40 +46,35 @@ def validate_jsonl_file(jsonl_path: str, all_pdf_files: list[str]):
                 raise ValueError(f"Missing required fields in line {line_num} of {jsonl_path}: {data}")
 
             rule_id = data["id"]
-
             if rule_id in rule_ids:
                 raise ValueError(f"Duplicate rule {rule_id} in {jsonl_path}")
             else:
                 rule_ids.add(rule_id)
 
-            # Make sure the document referenced exists
+            # Make sure the referenced PDF exists
             if data["pdf"] not in all_pdf_basenames:
                 raise ValueError(f"Missing pdf {data['pdf']} referenced by {rule_id} in {jsonl_path} line {line_num}")
 
-            # Additional validations depending on type
+            # Additional validations depending on rule type
             rule_type = data["type"]
             if rule_type in ("present", "absent"):
                 if "text" not in data:
                     raise ValueError(f"'text' field required for rule type '{rule_type}' in {jsonl_path} line {line_num}")
             elif rule_type == "order":
-                # Check that anchor is present, and that either 'before' or 'after' is present
                 if "before" not in data:
                     raise ValueError(f"'before' field required for rule type 'order' in {jsonl_path} line {line_num}")
                 if len(data["before"]) < 10:
-                    raise ValueError(f"'before' field too short {jsonl_path} line {line_num}")
+                    raise ValueError(f"'before' field too short in {jsonl_path} line {line_num}")
                 if "after" not in data:
-                    raise ValueError(f"'after' required for rule type 'order' in {jsonl_path} line {line_num}")
+                    raise ValueError(f"'after' field required for rule type 'order' in {jsonl_path} line {line_num}")
                 if len(data["after"]) < 10:
-                    raise ValueError(f"'after' field too short {jsonl_path} line {line_num}")
+                    raise ValueError(f"'after' field too short in {jsonl_path} line {line_num}")
             else:
                 raise ValueError(f"Unknown rule type '{rule_type}' in {jsonl_path} line {line_num}")
 
-            # If everything looks good, add to the rules list
             rules.append(data)
-
     return rules
 
-
 def run_rule(rule, md_file_path: str) -> (bool, str):
     """
     Run the given rule on the content of the provided .md file.
@@ -95,9 +92,7 @@ def run_rule(rule, md_file_path: str) -> (bool, str):
     if rule_type in ("present", "absent"):
         reference_query = rule["text"]
         threshold = rule.get("threshold", 1.0)
-
         best_ratio = fuzz.partial_ratio(reference_query, md_content) / 100.0
-
         if rule_type == "present":
             if best_ratio >= threshold:
                 return (True, "")
@@ -109,96 +104,96 @@ def run_rule(rule, md_file_path: str) -> (bool, str):
             else:
                 return (False, f"Expected '{reference_query[:40]}...' with threshold {threshold} but best match ratio was {best_ratio:.3f}")
     elif rule_type == "order":
-        # Implement a simple ordering check: ensure that the anchor text appears,
-        # and if 'before' is specified, it must appear before the anchor;
-        # if 'after' is specified, it must appear after the anchor.
         before = rule.get("before")
         after = rule.get("after")
         threshold = rule.get("threshold", 1.0)
-
         max_l_dist = round((1.0 - threshold) * len(before))
-
         before_matches = find_near_matches(before, md_content, max_l_dist=max_l_dist)
         after_matches = find_near_matches(after, md_content, max_l_dist=max_l_dist)
-
         if not before_matches:
-            return (False, f"'before' search text '{before[:40]}...' does not appear in parse with max_l_dist {max_l_dist}")
+            return (False, f"'before' search text '{before[:40]}...' not found with max_l_dist {max_l_dist}")
-        
         if not after_matches:
-            return (False, f"'after' search text '{after[:40]}...' does not appear in parse with max_l_dist {max_l_dist}")
+            return (False, f"'after' search text '{after[:40]}...' not found with max_l_dist {max_l_dist}")
-        
-        # Go through each combination of matches and see if there exists one where the before .start is sooner than the after .start
         for before_match, after_match in itertools.product(before_matches, after_matches):
             if before_match.start < after_match.start:
                 return (True, "")
-
+        return (False, f"Could not find a location where '{before[:40]}...' appears before '{after[:40]}...'.")
-        return (False, f"Could not find a place in the text where '{before[:40]}...' appears before '{after[:40]}...'.")
-
     else:
         raise NotImplementedError(f"Rule type '{rule_type}' is not implemented.")
 
-
 def evaluate_candidate(candidate_folder: str, all_rules: list, pdf_basenames: list[str]):
     """
-    For the candidate folder (pipeline tool output), first validate that it contains
+    For the candidate folder (pipeline tool output), validate that it contains at least one .md file
-    a .md file for every PDF in the pdf folder. Then, run each rule against the corresponding
+    (i.e. repeated generations like _1.md, _2.md, etc.) for every PDF in the pdf folder.
-    .md file.
+    Then, run each rule against all corresponding .md files and average the results.
     
     Returns a tuple:
-        (num_passed, total_rules, candidate_errors, rule_failures, rule_type_breakdown)
+      (overall_score, total_rules, candidate_errors, rule_failures, rule_type_breakdown)
-    where:
-      - candidate_errors is a list of error strings (e.g. missing files or exceptions)
-      - rule_failures is a list of rule failure messages (a rule returning False is not an error)
-      - rule_type_breakdown is a dict with rule type as key and a tuple (passed, total) as value
       
-    NOTE: A rule returning False is not considered an 'error' but simply a rule failure.
+      - overall_score: Average fraction of rules passed (averaged over repeats and rules).
-          Only exceptions and missing files are treated as candidate errors.
+      - total_rules: Total number of rules evaluated.
-          The rule_type_breakdown is added for a detailed breakdown of performance per rule type.
+      - candidate_errors: List of candidate errors (e.g. missing files).
+      - rule_failures: List of failure messages for rules not passing on all repeats.
+      - rule_type_breakdown: Dictionary mapping rule type to list of average pass ratios for rules of that type.
     """
     candidate_errors = []
     rule_failures = []
-    rule_type_breakdown = {}  # key: rule type, value: [passed_count, total_count]
+    rule_type_breakdown = {}  # key: rule type, value: list of average pass ratios
     candidate_name = os.path.basename(candidate_folder)
-    num_passed = 0
-    total_rules = 0
 
-    # Validate that a .md file exists for every PDF.
+    # Map each PDF to its corresponding MD repeats (e.g., doc1_1.md, doc1_2.md, etc.)
+    pdf_to_md_files = {}
     for pdf_name in pdf_basenames:
-        # Change .pdf extension to .md (assumes pdf_name ends with .pdf)
+        md_base = os.path.splitext(pdf_name)[0]
-        md_name = os.path.splitext(pdf_name)[0] + ".md"
+        md_pattern = os.path.join(candidate_folder, f"{md_base}_*.md")
-        md_path = os.path.join(candidate_folder, md_name)
+        md_files = glob.glob(md_pattern)
-        if not os.path.exists(md_path):
+        if not md_files:
-            candidate_errors.append(f"Candidate '{candidate_name}' is missing {md_name} corresponding to {pdf_name}.")
+            candidate_errors.append(
+                f"Candidate '{candidate_name}' is missing MD repeats for {pdf_name} (expected files matching {md_base}_*.md)."
+            )
+        else:
+            pdf_to_md_files[pdf_name] = md_files
 
-    # If there are missing .md files, we don't run the rules.
     if candidate_errors:
-        return (0, len(all_rules), candidate_errors, rule_failures, rule_type_breakdown)
+        return (0.0, len(all_rules), candidate_errors, rule_failures, rule_type_breakdown)
 
-    # Evaluate rules. Each rule references a PDF (e.g., "doc1.pdf"), and we expect the candidate to have "doc1.md".
+    total_rule_score = 0.0
+
+    # Evaluate each rule. Each rule references a PDF (e.g., "doc1.pdf") so we get all its MD repeats.
     for rule in all_rules:
         rule_type = rule["type"]
-        # Initialize breakdown counts for this rule type if not already
         if rule_type not in rule_type_breakdown:
-            rule_type_breakdown[rule_type] = [0, 0]
+            rule_type_breakdown[rule_type] = []
-        rule_type_breakdown[rule_type][1] += 1  # increment total count
-
         pdf_name = rule["pdf"]
-        md_name = os.path.splitext(pdf_name)[0] + ".md"
+        md_base = os.path.splitext(pdf_name)[0]
-        md_path = os.path.join(candidate_folder, md_name)
+        md_files = pdf_to_md_files.get(pdf_name, [])
-        total_rules += 1
+        if not md_files:
+            continue  # Should not occur due to earlier check.
+        repeat_passes = 0
+        num_repeats = 0
+        explanations = []
+        for md_path in md_files:
+            num_repeats += 1
             try:
                 passed, explanation = run_rule(rule, md_path)
                 if passed:
-                num_passed += 1
+                    repeat_passes += 1
-                rule_type_breakdown[rule_type][0] += 1  # increment passed count
                 else:
-                # A rule returning False is recorded as a rule failure, not an error.
+                    explanations.append(explanation)
-                rule_failures.append(f"Rule {rule.get('id')} on {md_name} failed: {explanation}")
             except Exception as e:
-            # Exceptions are considered candidate errors.
+                candidate_errors.append(f"Error running rule {rule.get('id')} on {md_path}: {e}")
-            candidate_errors.append(f"Error running rule {rule.get('id')} on {md_name}: {e}")
+                explanations.append(str(e))
+        rule_avg = repeat_passes / num_repeats if num_repeats > 0 else 0.0
+        total_rule_score += rule_avg
+        if rule_avg < 1.0:
+            rule_failures.append(
+                f"Rule {rule.get('id')} on {md_base} average pass ratio: {rule_avg:.3f} ({repeat_passes}/{num_repeats} repeats passed). "
+                f"Example explanation: {explanations[0] if explanations else 'No explanation'}"
+            )
+        rule_type_breakdown[rule_type].append(rule_avg)
 
-    return (num_passed, total_rules, candidate_errors, rule_failures, rule_type_breakdown)
+    overall_score = total_rule_score / len(all_rules) if all_rules else 0.0
+    return (overall_score, len(all_rules), candidate_errors, rule_failures, rule_type_breakdown)
 
 def main():
     parser = argparse.ArgumentParser(description="Run OLMOCR Bench.")
@@ -224,7 +219,7 @@ def main():
     # Get PDF basenames (e.g. "doc1.pdf")
     pdf_basenames = [os.path.basename(p) for p in all_pdf_files]
 
-    # Find .jsonl files in the input folder and validate them
+    # Find and validate .jsonl files in the input folder
     jsonl_files = glob.glob(os.path.join(input_folder, "*.jsonl"))
     if not jsonl_files:
         print(f"Error: No .jsonl files found in {input_folder}.", file=sys.stderr)
@@ -260,8 +255,8 @@ def main():
     print("\nRunning rules for each candidate:")
     for candidate in candidate_folders:
         candidate_name = os.path.basename(candidate)
-        num_passed, total_rules, candidate_errors, rule_failures, rule_type_breakdown = evaluate_candidate(candidate, all_rules, pdf_basenames)
+        overall_score, total_rules, candidate_errors, rule_failures, rule_type_breakdown = evaluate_candidate(candidate, all_rules, pdf_basenames)
-        summary.append((candidate_name, num_passed, total_rules, candidate_errors, rule_failures, rule_type_breakdown))
+        summary.append((candidate_name, overall_score, total_rules, candidate_errors, rule_failures, rule_type_breakdown))
         print(f"\nCandidate: {candidate_name}")
         if candidate_errors:
             for err in candidate_errors:
@@ -270,23 +265,24 @@ def main():
             if rule_failures:
                 for fail in rule_failures:
                     print(f"  [FAIL] {fail}")
-            print(f"  Passed {num_passed} out of {total_rules} rules.")
+            print(f"  Average Score: {overall_score * 100:.1f}% over {total_rules} rules.")
 
-    # Print a final summary (if only rule failures occurred, we output the score and breakdown)
+    # Print final summary with breakdown by rule type
     print("\n" + "="*50)
     print("Final Summary:")
-    for candidate_name, num_passed, total_rules, candidate_errors, _, rule_type_breakdown in summary:
+    for candidate_name, overall_score, total_rules, candidate_errors, _, rule_type_breakdown in summary:
         if candidate_errors:
             status = "FAILED (errors)"
         else:
-            status = f"{num_passed / total_rules * 100:0.1f}%"
+            status = f"{overall_score * 100:0.1f}%"
-        print(f"{candidate_name:20s} : {num_passed:3d}/{total_rules:3d} rules passed - {status}")
+        print(f"{candidate_name:20s} : Average Score: {overall_score * 100:0.1f}% over {total_rules:3d} rules - {status}")
         print("  Breakdown by rule type:")
-        for rtype, counts in rule_type_breakdown.items():
+        for rtype, scores in rule_type_breakdown.items():
-            passed_count, total_count = counts
+            if scores:
-            percentage = passed_count / total_count * 100 if total_count else 0
+                avg = sum(scores) / len(scores) * 100
-            print(f"    {rtype:8s}: {passed_count:2d}/{total_count:2d} rules passed ({percentage:0.1f}%)")
+            else:
-
+                avg = 0.0
+            print(f"    {rtype:8s}: {avg:0.1f}% average pass rate over {len(scores)} rules")
     print("="*50)
 
 if __name__ == "__main__":

olmocr/bench/convert.py

@@ -1,39 +1,90 @@
 import argparse
 import os
 import glob
-
+import importlib
 from tqdm import tqdm
 
-# Import all of the runners
+def parse_method_arg(method_arg):
-from olmocr.bench.runners.run_gotocr import run_gotocr
+    """
-from olmocr.bench.runners.run_marker import run_marker
+    Parse a method configuration string of the form:
-
+       method_name[:key=value[:key2=value2...]]
-# Goes through each pdf in the data folder, and converts them with each provided method
+    Returns:
+       (method_name, kwargs_dict)
+    """
+    parts = method_arg.split(":")
+    name = parts[0]
+    kwargs = {}
+    for extra in parts[1:]:
+        if "=" in extra:
+            key, value = extra.split("=", 1)
+            try:
+                converted = int(value)
+            except ValueError:
+                try:
+                    converted = float(value)
+                except ValueError:
+                    converted = value
+            kwargs[key] = converted
+        else:
+            raise ValueError(f"Extra argument '{extra}' is not in key=value format")
+    return name, kwargs
 
 if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Run PDF conversion using specified OCR methods and extra parameters."
+    )
+    parser.add_argument(
+        "methods",
+        nargs="+",
+        help="Methods to run in the format method[:key=value ...]. "
+             "Example: gotocr mineru:temperature=2 marker:runs=3"
+    )
+    parser.add_argument(
+        "--repeats",
+        type=int,
+        default=1,
+        help="Number of times to repeat the conversion for each PDF."
+    )
+    args = parser.parse_args()
+
+    # Mapping of method names to a tuple: (module path, function name)
+    available_methods = {
+        "gotocr": ("olmocr.bench.runners.run_gotocr", "run_gotocr"),
+        "marker": ("olmocr.bench.runners.run_marker", "run_marker"),
+        "mineru": ("olmocr.bench.runners.run_mineru", "run_mineru"),
+    }
+
+    # Build config by importing only requested methods.
+    config = {}
+    for method_arg in args.methods:
+        method_name, extra_kwargs = parse_method_arg(method_arg)
+        if method_name not in available_methods:
+            parser.error(f"Unknown method: {method_name}. "
+                         f"Available methods: {', '.join(available_methods.keys())}")
+        module_path, function_name = available_methods[method_name]
+        # Dynamically import the module and get the function.
+        module = importlib.import_module(module_path)
+        function = getattr(module, function_name)
+        config[method_name] = {
+            "method": function,
+            "kwargs": extra_kwargs
+        }
+
     data_directory = os.path.join(os.path.dirname(__file__), "sample_data")
     pdf_directory = os.path.join(data_directory, "pdfs")
 
-    config = {
+    # Process each PDF using each specified method and repeat the conversion as needed.
-        "marker": {
-            "method": run_marker
-        },
-
-        "got_ocr": {
-            "method": run_gotocr,
-            "temperature": 0.0,
-        },
-    }
-
-
     for candidate in config.keys():
-        print(f"Starting conversion using {candidate}")
+        print(f"Starting conversion using {candidate} with kwargs: {config[candidate]['kwargs']}")
-        os.makedirs(os.path.join(data_directory, candidate), exist_ok=True)
+        candidate_output_dir = os.path.join(data_directory, candidate)
+        os.makedirs(candidate_output_dir, exist_ok=True)
 
         for pdf_path in tqdm(glob.glob(os.path.join(pdf_directory, "*.pdf")), desc=candidate):
-            markdown = config[candidate]["method"](pdf_path, page_num=1)
+            base_name = os.path.basename(pdf_path).replace(".pdf", "")
-
+            # Repeat the conversion as many times as specified.
-            with open(os.path.join(data_directory, candidate, os.path.basename(pdf_path).replace(".pdf", ".md")), "w") as out_f:
+            for i in range(1, args.repeats + 1):
+                markdown = config[candidate]["method"](pdf_path, page_num=1, **config[candidate]["kwargs"])
+                output_filename = f"{base_name}_{i}.md"
+                output_path = os.path.join(candidate_output_dir, output_filename)
+                with open(output_path, "w") as out_f:
                     out_f.write(markdown)
-
-            

olmocr/bench/runners/run_mineru.py

@@ -8,20 +8,7 @@ from magic_pdf.model.doc_analyze_by_custom_model import doc_analyze
 from magic_pdf.config.enums import SupportedPdfParseMethod
 
 
-def run(pdf_folder):
+def run_mineru(pdf_path: str, page_num: int=1) -> str:
-    """
-    Convert all PDF files in the specified folder to markdown using MinerU.
-    For each PDF file, the script outputs markdown files along with visual and JSON outputs.
-    The outputs are saved in a folder called "mineru" (with an "images" subfolder) 
-    located in the same parent directory as pdf_folder.
-    
-    :param pdf_folder: Path to the folder containing PDF files.
-    """
-    # Resolve absolute paths
-    pdf_folder = os.path.abspath(pdf_folder)
-    parent_dir = os.path.dirname(pdf_folder)
-    output_folder = os.path.join(parent_dir, "mineru")
-    image_output_folder = os.path.join(output_folder, "images")
    
     # Create output directories if they don't exist
     os.makedirs(image_output_folder, exist_ok=True)
@@ -31,19 +18,6 @@ def run(pdf_folder):
     image_writer = FileBasedDataWriter(image_output_folder)
     md_writer = FileBasedDataWriter(output_folder)
 
-    # List all PDF files in the provided folder
-    pdf_files = [
-        os.path.join(pdf_folder, filename)
-        for filename in os.listdir(pdf_folder)
-        if filename.lower().endswith(".pdf")
-    ]
-
-    for pdf_path in pdf_files:
-        print(f"Processing {pdf_path}...")
-        # Get file name without suffix for naming outputs
-        pdf_file_name = os.path.basename(pdf_path)
-        name_without_suff = pdf_file_name.split(".")[0]
-
     # Read the PDF file bytes
     reader = FileBasedDataReader("")
     pdf_bytes = reader.read(pdf_path)
@@ -67,10 +41,13 @@ def run(pdf_folder):
     md_file_name = f"{name_without_suff}.md"
     pipe_result.dump_md(md_writer, md_file_name, image_dir_basename)
 
+    with open(os.path.join(output_folder, md_file_name), "r") as f:
+        md_data = f.read()
+
     # Remove useless image folder
     shutil.rmtree(image_output_folder)
 
-        print(f"Finished processing {pdf_file_name}. Outputs saved to {output_folder}.")
+    return md_data
 
 
 if __name__ == "__main__":