enabled no_patches arg and fixed some directory creations

README.md

@@ -21,7 +21,6 @@ Convert Helper for Histopathological / Cytopathological Machine Learning Tasks
 3. Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.
 
 [WSIPatcher](https://github.com/tand826/WSIPatcher) will give you GUI.
-[Command Helper](https://tand826.github.io/wsiprocess_command_line_helper) will recommend commands to run.
 
 # Installation
 
@@ -109,21 +108,21 @@ patcher.get_patch_parallel(target_classes)
 ```
 
 
-### As a command line tool
+### As a command line tool (recommended)
 
 #### basic flow
 
 ```bash
-wsiprocess xxx.tiff method --annotation xxx.xml
+wsiprocess [your method] xxx.tiff --annotation xxx.xml
 ```
 
 #### Extract patches with mask of foreground area. The mask has pixels with 1 as foreground which are originally from 10 to 230 in the scale of 0-255, and pixels with 0 as background which are originally from 0 to 10 and from 230 to 255.
 
 ```bash
-wsiprocess xxx.tif none -oa 0.01 -mm 10-230 -of 0.01 -ep
+wsiprocess none xxx.tif -oa 0.01 -mm 10-230 -of 0.01 -ep
 ```
 
-- Need recommendation for choice of arguments? -> [Command Helper](https://tand826.github.io/wsiprocess_command_line_helper). This is for v0.1. Now wsiprocess has more options. Type `wsiprocess` to see options.
+- Need recommendation for choice of arguments? Type `wsiprocess -h` or `wsiprocess [your method] -h` to see options.
 
 ### As a docker command line tool (not working on)
 
@@ -274,10 +273,13 @@ pytest tests.py
 # Citation
 
 ```
-@article{wsiprocess,
-    Author = {Takumi Ando},
-    Title = {WSIPROCESS - Whole Slide Image Processing Library for Histopathological / Cytopathological Machine Learning Tasks},
-    Url = {https://github.com/tand826/wsiprocess},
-    Year = {2019}
+@misc{https://doi.org/10.5281/zenodo.3887428,
+  doi = {10.5281/ZENODO.3887428},
+  url = {https://zenodo.org/record/3887428},
+  author = {{Takumi Ando}},
+  title = {tand826/wsiprocess: version 0.4},
+  publisher = {Zenodo},
+  year = {2020},
+  copyright = {Open Access}
 }
 ```

tests/tests.py

@@ -45,7 +45,7 @@ class Params:
     offset_x = OFFSET_X[0]
     offset_y = OFFSET_Y[0]
     magnification = MAGNIFICATIONS[0]
-    extract_patches = True
+    no_patches = False
     voc_style = VOC_STYLE[0]
     coco_style = COCO_STYLE[0]
     yolo_style = YOLO_STYLE[0]
@@ -77,7 +77,7 @@ def cli(params):
         offset_y=params.offset_y,
         on_foreground=params.on_foreground,
         on_annotation=params.on_annotation,
-        extract_patches=params.extract_patches)
+        no_patches=params.no_patches)
     patcher.get_patch_parallel(annotation.classes)
     if params.voc_style or params.coco_style or params.yolo_style:
         converter = wp.converter(params.save_to/slide.filestem, params.save_to, params.ratio)

wsiprocess/__init__.py

@@ -4,4 +4,4 @@
 from .rule import Rule as rule
 from .converter import Converter as converter
 
-__version__ = "0.3.1"
+__version__ = "0.4"

wsiprocess/cli.py

@@ -11,11 +11,6 @@ def set_base_parser(self):
         self.base_parser = argparse.ArgumentParser(
             description="wsiprocess command line tool")
 
-    def set_wsi_arg(self):
-        self.base_parser.add_argument(
-            "wsi", type=str,
-            help="Path to the target wsi.")
-
     def set_common_args(self, parser):
         """ Common Arguments """
         parser.add_argument(
@@ -45,9 +40,17 @@ def set_common_args(self, parser):
         parser.add_argument(
             "-fs", "--finished_sample", action="store_true",
             help="Generate samples at the end of the process.")
+        parser.add_argument(
+            "-np", "--no_patches", action="store_true",
+            help="Patcher run without extracting patches.")
         parser.add_argument(
             "-ep", "--extract_patches", action="store_true",
-            help="Extract the patches and save them as images.")
+            help="[Not Available]Extract the patches and save them as images.")
+
+    def set_wsi_arg(self, parser):
+        parser.add_argument(
+            "wsi", type=str,
+            help="Path to the target wsi.")
 
     def add_annotation_args(self, parser, slide_is_sparse=False):
         parser.add_argument(
@@ -94,6 +97,7 @@ def set_none_args(self):
         parser_none = self.method_args.add_parser(
             "none",
             help="Arguments for not specific method.")
+        self.set_wsi_arg(parser_none)
         self.add_on_foreground(parser_none)
         self.add_binarization_method(parser_none)
         self.set_common_args(parser_none)
@@ -103,6 +107,7 @@ def set_classification_args(self):
         parser_cls = self.method_args.add_parser(
             "classification",
             help="Arguments for classification tasks.")
+        self.set_wsi_arg(parser_cls)
         self.add_annotation_args(parser_cls)
         self.set_common_args(parser_cls)
 
@@ -111,6 +116,8 @@ def set_detection_args(self):
         parser_det = self.method_args.add_parser(
             "detection",
             help="Arguments for detection tasks.")
+        self.set_wsi_arg(parser_det)
+
         parser_det.add_argument(
             "-vo", "--voc_style", action="store_true",
             help="Output as VOC style.")
@@ -132,14 +139,14 @@ def set_segmentation_args(self):
             "segmentation",
             help="Arguments for segmentation tasksk."
         )
+        self.set_wsi_arg(parser_seg)
         self.add_annotation_args(parser_seg)
         self.set_common_args(parser_seg)
 
     def build_args(self, command):
         """ Base Parser """
         self.set_base_parser()
 
-        self.set_wsi_arg()
         self.set_method_args()
         self.set_none_args()
         self.set_classification_args()
@@ -179,7 +186,7 @@ def main(command=None):
     rule = wp.rule(args.rule) if hasattr(args, "rule") else False
     annotation = process_annotation(args, slide, rule)
 
-    if hasattr(args, "export_thumbs"):
+    if hasattr(args, "export_thumbs") and args.export_thumbs:
         thumbs_dir = args.save_to/slide.filestem/"thumbs"
         if not thumbs_dir.exists():
             thumbs_dir.mkdir(parents=True)
@@ -201,7 +208,7 @@ def main(command=None):
         offset_y=args.offset_y,
         start_sample=args.start_sample,
         finished_sample=args.finished_sample,
-        extract_patches=args.extract_patches)
+        no_patches=args.no_patches)
     patcher.get_patch_parallel(annotation.classes)
 
     if args.method == "detection":

wsiprocess/patcher.py

@@ -39,8 +39,10 @@ class Patcher:
             Patcher starting.
         finished_sample (bool, optional): Whether to save sample patches on
             Patcher finished its work.
-        extract_patches (bool, optional): Whether to save patches when Patcher
-            runs.
+        extract_patches (bool, optional): This is deprecated because unless
+            "no_patches" is set, Patcher extracts patches.
+        no_patches (bool, optional): If set, Patcher runs without extracting
+            patches and saves them to disk.
 
     Attributes:
         slide (wsiprocess.slide.Slide): Slide object.
@@ -70,6 +72,7 @@ class Patcher:
         finished_sample (bool): Whether to save sample patches on Patcher
             finish.
         extract_patches (bool): Whether to save patches when Patcher runs.
+        no_patches (bool): Whether to save patches when Patcher runs.
 
         x_lefttop (list): Offsets of patches to the x-axis direction except for
             the right edge.
@@ -87,7 +90,7 @@ def __init__(
             patch_width=256, patch_height=256, overlap_width=0,
             overlap_height=0, offset_x=0, offset_y=0, on_foreground=0.5,
             on_annotation=1., start_sample=True, finished_sample=True,
-            extract_patches=True):
+            no_patches=False):
         Verify.verify_sizes(
             slide.wsi_width, slide.wsi_height, patch_width, patch_height,
             overlap_width, overlap_height)
@@ -114,7 +117,7 @@ def __init__(
 
         self.start_sample = start_sample
         self.finished_sample = finished_sample
-        self.extract_patches = extract_patches
+        self.no_patches = no_patches
 
         self.on_foreground = on_foreground
         self.annotation = annotation
@@ -131,7 +134,7 @@ def __init__(
 
         self.result = {"result": []}
         self.verify = Verify(save_to, self.filestem, method,
-                             start_sample, finished_sample, extract_patches)
+                             start_sample, finished_sample, no_patches)
         self.verify.verify_dirs()
 
     def __str__(self):
@@ -335,7 +338,7 @@ def save_results(self):
         self.result["offset_y"] = self.offset_y
         self.result["start_sample"] = self.start_sample
         self.result["finished_sample"] = self.finished_sample
-        self.result["extract_patches"] = self.extract_patches
+        self.result["no_patches"] = self.no_patches
         self.result["on_foreground"] = self.on_foreground
         self.result["on_annotation"] = self.on_annotation
         self.result["save_to"] = str(Path(self.save_to).absolute())
@@ -365,12 +368,13 @@ def get_patch(self, x, y, classes=False):
                     on_annotation_classes.append(cls)
         else:
             on_annotation_classes = ["foreground"]
-        if self.extract_patches:
-            patch = self.slide.slide.crop(x, y, self.p_width, self.p_height)
-            for cls in on_annotation_classes:
+        patch = self.slide.slide.crop(x, y, self.p_width, self.p_height)
+        for cls in on_annotation_classes:
+            if not self.no_patches:
                 patch.jpegsave(
-                    "{}/{}/patches/{}/{:06}_{:06}.jpg".format(self.save_to, self.filestem, cls, x, y))
-                self.save_patch_result(x, y, cls)
+                    "{}/{}/patches/{}/{:06}_{:06}.jpg".format(
+                        self.save_to, self.filestem, cls, x, y))
+            self.save_patch_result(x, y, cls)
 
     def get_patch_parallel(self, classes=False, cores=-1):
         """Run get_patch() in parallel.
@@ -380,7 +384,7 @@ def get_patch_parallel(self, classes=False, cores=-1):
             cores (int): Threads to run. -1 means same as the number of cores.
         """
         for cls in classes:
-            if self.extract_patches:
+            if not self.no_patches:
                 self.verify.verify_dir(
                     "{}/{}/patches/{}".format(self.save_to, self.filestem, cls))
             if self.method == "segmentation":

wsiprocess/verify.py

@@ -19,7 +19,9 @@ class Verify:
         start_sample (bool): Whether to save sample patches on Patcher start.
         finished_sample (bool): Whether to save sample patches on Patcher
             finish.
-        extract_patches (bool): Whether to save patches when Patcher runs.
+        extract_patches (bool): [Deleted]Whether to save patches when Patcher
+            runs.
+        no_patches (bool): Whether to save patches when Patcher runs.
 
     Attributes:
         save_to (str): The root of the output directory.
@@ -29,34 +31,34 @@ class Verify:
         start_sample (bool): Whether to save sample patches on Patcher start.
         finished_sample (bool): Whether to save sample patches on Patcher
             finish.
-        extract_patches (bool): Whether to save patches when Patcher runs.
+        extract_patches (bool): [Deleted]Whether to save patches when Patcher
+            runs.
+        no_patches (bool): Whether to save patches when Patcher runs.
     """
 
     def __init__(
             self, save_to, filestem, method, start_sample,
-            finished_sample, extract_patches):
+            finished_sample, no_patches):
         self.save_to = save_to
         self.filestem = filestem
         self.method = method
         self.start_sample = start_sample
         self.finished_sample = finished_sample
-        self.extract_patches = extract_patches
+        self.no_patches = no_patches
 
     def verify_dirs(self):
         """Ensure the output directories exists for each tasks.
         """
         base_dir = Path(self.save_to)/self.filestem
         self.verify_dir(base_dir)
-        if self.method == "none":
+        if self.method == "none" and not self.no_patches:
             self.verify_dir(base_dir/"patches"/"foreground")
         if self.method == "segmentation":
             self.verify_dir(base_dir/"masks")
         if self.start_sample:
             self.verify_dir(base_dir/"start_sample")
         if self.finished_sample:
             self.verify_dir(base_dir/"finished_sample")
-        if self.extract_patches:
-            self.verify_dir(base_dir/"patches")
 
     @staticmethod
     def verify_dir(path):