new version 2.3.1 (#509)

Co-authored-by: Zykina (Bogatenkova) Anastasiya <bogatenkova.anastasiya@mail.ru>
Co-authored-by: Gabriele Conte <100914559+GabrieleConte@users.noreply.github.com>
Co-authored-by: Alexander Golodkov <55749660+alexander1999-hub@users.noreply.github.com>
Co-authored-by: Andrey Mikhailov <mikhailov@icc.ru>
Co-authored-by: alexander1999-hub <golodkov.ao@phystech.edu>

VERSION

@@ -1 +1 @@
-2.3
+2.3.1

dedoc/api/web/index.html

@@ -122,7 +122,7 @@ <h4>Tables handling </h4>
 
         <div class="parameters">
             <h4>PDF handling</h4>
-            <details><summary>pdf_with_text_layer, fast_textual_layer_detection, language, pages, is_one_column_document, document_orientation, need_header_footer_analysis, need_binarization</summary>
+            <details><summary>pdf_with_text_layer, fast_textual_layer_detection, language, pages, is_one_column_document, document_orientation, need_header_footer_analysis, need_binarization, need_gost_frame_analysis</summary>
                 <br>
                 <p>
                     <label>

dedoc/data_structures/cell_with_meta.py

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional
 
 from dedoc.api.schema.cell_with_meta import CellWithMeta as ApiCellWithMeta
 from dedoc.data_structures.annotation import Annotation
@@ -20,14 +20,14 @@ class CellWithMeta(Serializable):
     :vartype rowspan: int
     :vartype invisible: bool
     """
-    def __init__(self, lines: List[LineWithMeta], colspan: int = 1, rowspan: int = 1, invisible: bool = False) -> None:
+    def __init__(self, lines: Optional[List[LineWithMeta]], colspan: int = 1, rowspan: int = 1, invisible: bool = False) -> None:
         """
         :param lines: textual lines of the cell
         :param colspan: number of columns to span like in HTML format
         :param rowspan: number of rows to span like in HTML format
         :param invisible: indicator for displaying or hiding cell text
         """
-        self.lines: List[LineWithMeta] = lines
+        self.lines: List[LineWithMeta] = [] if lines is None else lines
         self.colspan: int = colspan
         self.rowspan: int = rowspan
         self.invisible: bool = invisible

dedoc/readers/article_reader/article_reader.py

@@ -28,6 +28,9 @@ def __init__(self, config: Optional[dict] = None) -> None:
         else:
             self.grobid_url = f"http://{os.environ.get('GROBID_HOST', 'localhost')}:{os.environ.get('GROBID_PORT', '8070')}"
         self.url = f"{self.grobid_url}/api/processFulltextDocument"
+
+        auth_key = os.environ.get("GROBID_AUTH_KEY", "")
+        self.request_headers = {"Authorization": auth_key} if auth_key else {}
         self.grobid_is_alive = False
 
     def read(self, file_path: str, parameters: Optional[dict] = None) -> UnstructuredDocument:
@@ -48,7 +51,7 @@ def read(self, file_path: str, parameters: Optional[dict] = None) -> Unstructure
         with open(file_path, "rb") as file:
             files = {"input": file}
             try:
-                response = requests.post(self.url, files=files, data={"teiCoordinates": "figure"})
+                response = requests.post(self.url, files=files, data={"teiCoordinates": "figure"}, headers=self.request_headers)
                 if response.status_code != 200:
                     warning = f"GROBID returns code {response.status_code}."
                     self.logger.warning(warning)
@@ -106,7 +109,7 @@ def __update_grobid_alive(self, grobid_url: str, max_attempts: int = 2) -> None:
         attempt = max_attempts
         while attempt > 0:
             try:
-                response = requests.get(f"{grobid_url}/api/isalive")
+                response = requests.get(f"{grobid_url}/api/isalive", headers=self.request_headers)
                 if response.status_code == 200:
                     self.logger.info(f"GROBID up on {grobid_url}.")
                     self.grobid_is_alive = True

dedoc/readers/docx_reader/numbering_extractor.py

@@ -75,9 +75,9 @@ def parse(self, xml: Tag, paragraph_properties: BaseProperties, run_properties:
             self.styles_extractor.parse(lvl_info.style_id, paragraph_properties, StyleType.NUMBERING)
         if lvl_info.pPr:
             change_paragraph_properties(paragraph_properties, lvl_info.pPr)
+        # run properties are applied only to the numbering text ("lvlText" content)
         if lvl_info.rPr:
             change_run_properties(run_properties, lvl_info.rPr)
-            change_run_properties(paragraph_properties, lvl_info.rPr)
 
         run_properties.text = text
         paragraph_properties.list_level = self.state.levels_count

dedoc/readers/pdf_reader/data_classes/tables/cell.py

@@ -3,10 +3,11 @@
 from dedocutils.data_structures import BBox
 
 from dedoc.data_structures.annotation import Annotation
+from dedoc.data_structures.cell_with_meta import CellWithMeta
 from dedoc.data_structures.line_with_meta import LineWithMeta
 
 
-class Cell:
+class Cell(CellWithMeta):
 
     @staticmethod
     def copy_from(cell: "Cell",
@@ -41,35 +42,27 @@ def shift(self, shift_x: int, shift_y: int, image_width: int, image_height: int)
         if self.con_coord:
             self.con_coord.shift(shift_x=shift_x, shift_y=shift_y)
 
-    def __init__(self,
-                 x_top_left: int,
-                 x_bottom_right: int,
-                 y_top_left: int,
-                 y_bottom_right: int,
-                 id_con: int = -1,
-                 lines: Optional[List[LineWithMeta]] = None,
-                 is_attribute: bool = False,
-                 is_attribute_required: bool = False,
-                 rotated_angle: int = 0,
-                 uid: str = None,
+    def __init__(self, x_top_left: int, x_bottom_right: int, y_top_left: int, y_bottom_right: int, id_con: int = -1, lines: Optional[List[LineWithMeta]] = None,
+                 is_attribute: bool = False, is_attribute_required: bool = False, rotated_angle: int = 0, uid: str = None,
                  contour_coord: Optional[BBox] = None) -> None:
+
         import uuid
 
         assert x_top_left <= x_bottom_right
         assert y_top_left <= y_bottom_right
+
+        self.lines = [] if lines is None else lines
+        super().__init__(lines)
+
         self.x_top_left = x_top_left
         self.x_bottom_right = x_bottom_right
         self.y_top_left = y_top_left
         self.y_bottom_right = y_bottom_right
         self.id_con = id_con
-        self.lines = [] if lines is None else lines
         self.is_attribute = is_attribute
         self.is_attribute_required = is_attribute_required
         self.rotated_angle = rotated_angle
         self.cell_uid = f"cell_{uuid.uuid1()}" if uid is None else uid
-        self.colspan = 1
-        self.rowspan = 1
-        self.invisible = False
         self.con_coord = contour_coord or BBox(0, 0, 0, 0)
 
     def __str__(self) -> str:

dedoc/readers/pdf_reader/data_classes/tables/location.py

@@ -10,6 +10,7 @@ def __init__(self, page_number: int, bbox: BBox, name: str = "", rotated_angle:
         self.page_number = page_number
         self.bbox = bbox
         self.name = name
+        # TODO put self.order (change LineWithLocation, PdfImageAttachment, ScanTable)
         self.rotated_angle = rotated_angle
 
     def shift(self, shift_x: int, shift_y: int) -> None:

dedoc/readers/pdf_reader/data_classes/tables/scantable.py

@@ -1,4 +1,4 @@
-from typing import Any, List
+from typing import Any, List, Optional
 
 from dedocutils.data_structures import BBox
 
@@ -10,7 +10,8 @@
 
 
 class ScanTable:
-    def __init__(self, page_number: int, matrix_cells: List[List[Cell]] = None, bbox: BBox = None, name: str = "", order: int = -1) -> None:
+    def __init__(self, page_number: int, matrix_cells: Optional[List[List[CellWithMeta]]] = None, bbox: Optional[BBox] = None,
+                 name: str = "", order: int = -1) -> None:
         self.matrix_cells = matrix_cells
         self.page_number = page_number
         self.locations = []
@@ -27,6 +28,15 @@ def extended(self, table: "ScanTable") -> None:
         # extend order
         self.order = max(self.order, table.order)
 
+    def check_on_cell_instance(self) -> bool:
+        if len(self.matrix_cells) == 0:
+            return False
+        if len(self.matrix_cells[0]) == 0:
+            return False
+        if not isinstance(self.matrix_cells[0][0], Cell):
+            return False
+        return True
+
     def to_table(self) -> Table:
         metadata = TableMetadata(page_id=self.page_number, uid=self.name, rotated_angle=self.location.rotated_angle)
         cells_with_meta = [[CellWithMeta.create_from_cell(cell) for cell in row] for row in self.matrix_cells]

dedoc/readers/pdf_reader/pdf_base_reader.py

@@ -2,7 +2,6 @@
 from collections import namedtuple
 from typing import Dict, Iterator, List, Optional, Set, Tuple
 
-import numpy as np
 from dedocutils.data_structures.bbox import BBox
 from numpy import ndarray
 
@@ -13,7 +12,7 @@
 from dedoc.readers.pdf_reader.data_classes.line_with_location import LineWithLocation
 from dedoc.readers.pdf_reader.data_classes.pdf_image_attachment import PdfImageAttachment
 from dedoc.readers.pdf_reader.data_classes.tables.scantable import ScanTable
-from dedoc.readers.pdf_reader.pdf_image_reader.table_recognizer.gost_frame_recognizer import GOSTFrameRecognizer
+
 
 ParametersForParseDoc = namedtuple("ParametersForParseDoc", [
     "orient_analysis_cells",
@@ -45,6 +44,7 @@ def __init__(self, *, config: Optional[dict] = None, recognized_extensions: Opti
 
         from dedoc.readers.pdf_reader.pdf_image_reader.line_metadata_extractor.metadata_extractor import LineMetadataExtractor
         from dedoc.readers.pdf_reader.pdf_image_reader.paragraph_extractor.scan_paragraph_classifier_extractor import ScanParagraphClassifierExtractor
+        from dedoc.readers.pdf_reader.pdf_image_reader.table_recognizer.gost_frame_recognizer import GOSTFrameRecognizer
         from dedoc.readers.pdf_reader.pdf_image_reader.table_recognizer.table_recognizer import TableRecognizer
         from dedoc.readers.pdf_reader.utils.line_object_linker import LineObjectLinker
         from dedoc.attachments_extractors.concrete_attachments_extractors.pdf_attachments_extractor import PDFAttachmentsExtractor
@@ -153,24 +153,24 @@ def _parse_document(self, path: str, parameters: ParametersForParseDoc) -> (
             metadata["rotated_page_angles"] = page_angles
         return all_lines_with_paragraphs, mp_tables, attachments, warnings, metadata
 
-    def _process_document_with_gost_frame(self, images: Iterator[np.ndarray], first_page: int, parameters: ParametersForParseDoc, path: str) -> \
-            Tuple[Tuple[List[LineWithLocation], List[ScanTable], List[PdfImageAttachment], List[float]], Dict[int, Tuple[np.ndarray, BBox, Tuple[int, ...]]]]:
+    def _process_document_with_gost_frame(self, images: Iterator[ndarray], first_page: int, parameters: ParametersForParseDoc, path: str) -> \
+            Tuple[Tuple[List[LineWithLocation], List[ScanTable], List[PdfImageAttachment], List[float]], Dict[int, Tuple[ndarray, BBox, Tuple[int, ...]]]]:
         from joblib import Parallel, delayed
         from dedoc.readers.pdf_reader.pdf_txtlayer_reader.pdf_txtlayer_reader import PdfTxtlayerReader
 
         gost_analyzed_images = Parallel(n_jobs=self.config["n_jobs"])(delayed(self.gost_frame_recognizer.rec_and_clean_frame)(image) for image in images)
         page_range = range(first_page, first_page + len(gost_analyzed_images))
         gost_analyzed_images = dict(zip(page_range, gost_analyzed_images))
         if isinstance(self, PdfTxtlayerReader):
-            self.gost_frame_boxes = dict(zip(page_range, [item[1] for item in gost_analyzed_images.values()]))
+            self.gost_frame_boxes = dict(zip(page_range, [(item[1], item[2]) for item in gost_analyzed_images.values()]))
         result = Parallel(n_jobs=self.config["n_jobs"])(
             delayed(self._process_one_page)(image, parameters, page_number, path) for page_number, (image, box, original_image_shape) in
             gost_analyzed_images.items()
         )
         return result, gost_analyzed_images
 
     def _shift_all_contents(self, lines: List[LineWithMeta], unref_tables: List[ScanTable], attachments: List[PdfImageAttachment],
-                            gost_analyzed_images: Dict[int, Tuple[np.ndarray, BBox, Tuple[int, ...]]]) -> None:
+                            gost_analyzed_images: Dict[int, Tuple[ndarray, BBox, Tuple[int, ...]]]) -> None:
         # shift unref_tables
         for scan_table in unref_tables:
             for location in scan_table.locations:

dedoc/readers/pdf_reader/pdf_image_reader/pdf_image_reader.py

@@ -3,6 +3,7 @@
 
 from numpy import ndarray
 
+from dedoc.data_structures.unstructured_document import UnstructuredDocument
 from dedoc.readers.pdf_reader.data_classes.line_with_location import LineWithLocation
 from dedoc.readers.pdf_reader.data_classes.pdf_image_attachment import PdfImageAttachment
 from dedoc.readers.pdf_reader.data_classes.tables.scantable import ScanTable
@@ -53,6 +54,9 @@ def __init__(self, *, config: Optional[dict] = None) -> None:
         self.binarizer = AdaptiveBinarizer()
         self.ocr = OCRLineExtractor(config=self.config)
 
+    def read(self, file_path: str, parameters: Optional[dict] = None) -> UnstructuredDocument:
+        return super().read(file_path, parameters)
+
     def _process_one_page(self,
                           image: ndarray,
                           parameters: ParametersForParseDoc,

dedoc/readers/pdf_reader/pdf_image_reader/table_recognizer/table_extractors/concrete_extractors/multipage_table_extractor.py

@@ -1,3 +1,4 @@
+import copy
 import logging
 from typing import List
 
@@ -155,24 +156,26 @@ def __is_one_table(self, t1: ScanTable, t2: ScanTable) -> bool:
         # condition 2. Exclusion of the duplicated header (if any)
         attr1 = TableAttributeExtractor.get_header_table(t1.matrix_cells)
         attr2 = TableAttributeExtractor.get_header_table(t2.matrix_cells)
+        t2_update = copy.deepcopy(t2)
         if TableAttributeExtractor.is_equal_attributes(attr1, attr2):
-            t2.matrix_cells = t2.matrix_cells[len(attr2):]
+            t2_update.matrix_cells = t2_update.matrix_cells[len(attr2):]
 
-        if len(t2.matrix_cells) == 0 or len(t1.matrix_cells) == 0:
+        if len(t2_update.matrix_cells) == 0 or len(t1.matrix_cells) == 0:
             return False
 
-        TableAttributeExtractor.clear_attributes(t2.matrix_cells)
+        TableAttributeExtractor.clear_attributes(t2_update.matrix_cells)
 
         # condition 3. Number of columns should be equal
-        if len(t1.matrix_cells[-1]) != len(t2.matrix_cells[0]):
+        if len(t1.matrix_cells[-1]) != len(t2_update.matrix_cells[0]):
             if self.config.get("debug_mode", False):
                 self.logger.debug("Different count column")
             return False
 
         # condition 4. Comparison of the widths of last and first rows
-        if not self.__is_equal_width_cells(t1.matrix_cells, t2.matrix_cells):
+        if t1.check_on_cell_instance() and t2_update.check_on_cell_instance() and not self.__is_equal_width_cells(t1.matrix_cells, t2_update.matrix_cells):
             if self.config.get("debug_mode", False):
                 self.logger.debug("Different width columns")
             return False
 
+        t2.matrix_cells = copy.deepcopy(t2_update.matrix_cells)  # save changes
         return True

dedoc/readers/pdf_reader/pdf_image_reader/table_recognizer/table_extractors/concrete_extractors/table_attribute_extractor.py

@@ -31,8 +31,22 @@ def is_equal_attributes(attr1: List[List[Cell]], attr2: List[List[Cell]], thr_si
 
         return True
 
+    @staticmethod
+    def check_have_attributes(matrix_table: List[List[Cell]]) -> bool:
+        if len(matrix_table) == 0:
+            return False
+        if len(matrix_table[0]) == 0:
+            return False
+        if not hasattr(matrix_table[0][0], "is_attribute"):
+            return False
+        return True
+
     @staticmethod
     def get_header_table(matrix_table: List[List[Cell]]) -> List[List[Cell]]:
+
+        if not TableAttributeExtractor.check_have_attributes(matrix_table):
+            return matrix_table[:1]
+
         header_rows = len(matrix_table)
         for (i, row) in enumerate(matrix_table):
             attrs = [cell for cell in row if cell.is_attribute]
@@ -44,6 +58,9 @@ def get_header_table(matrix_table: List[List[Cell]]) -> List[List[Cell]]:
 
     @staticmethod
     def clear_attributes(matrix_table: List[List[Cell]]) -> None:
+        if not TableAttributeExtractor.check_have_attributes(matrix_table):
+            return
+
         for row in matrix_table:
             for cell in row:
                 cell.is_attribute = False