1.0.1

.gitignore

@@ -172,6 +172,10 @@ examples/expected_results/registered_slides
 tests/tmp39
 tests/tmp310
 tests/tmp311
+tests/39
+tests/310
+tests/311
+tests/docker
 tests/test_difficult_cases.py
 tests/test_read_czi_jpgxr.py
 tests/test_tiler.py
@@ -197,3 +201,11 @@ Dockerfile_torch_debian
 torch_pyproject.toml
 
 tests/test_micro_rigid.py
+
+pip_poetry.lock
+
+pip_pyproject.toml
+
+docker_run_tests.sh
+
+docker_run_tests_by_line.sh

docs/changelog.rst

@@ -1,6 +1,11 @@
 Change Log
 **********
 
+Version 1.0.1 (October 6, 2023)
+-------------------------------------
+#. Bug fixes to functions related to saving slides as ome.tiff
+#. Address numba deprecation warnings
+
 Version 1.0.0 (October 4, 2023)
 -------------------------------------
 #. Added option for high resolution rigid registration using the :code:`micro_rigid_registrar.MicroRigidRegistrar` class. To use this option, pass an uninstantiated :code:`micro_rigid_registrar.MicroRigidRegistrar` to :code:`micro_rigid_registrar_cls` when initializing the :code:`Valis` object. This class refines the rigid registration by detecting and matching features in higher resolution images warped using the initial rigid transforms. This should result in more accurate rigid registration, error estimates, and hopefully fewer unwanted non-rigid deformations.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "valis-wsi"
-version = "1.0.0"
+version = "1.0.1"
 description = ""
 authors = ["Chandler Gatenbee <[email protected]>"]
 license = "MIT"

tests/test_examples.py

@@ -52,6 +52,7 @@
 
 import shutil
 import sys
+import os
 # sys.path.append("/Users/gatenbcd/Dropbox/Documents/image_processing/valis_project/valis")
 from valis import registration, valtils
 from valis.micro_rigid_registrar import MicroRigidRegistrar
@@ -74,11 +75,15 @@ def cnames_from_filename(src_f):
  f = valtils.get_name(src_f)
  return ["DAPI"] + f.split(" ")
 
-parent_dir = get_parent_dir()
+# parent_dir = get_parent_dir()
+parent_dir = "/Users/gatenbcd/Dropbox/Documents/image_processing/valis_project"
 datasets_src_dir = os.path.join(parent_dir, "valis/examples/example_datasets/")
-results_dst_dir = os.path.join(parent_dir, f"valis/tests/tmp{sys.version_info.major}{sys.version_info.minor}")
-
 
+in_container = sys.platform == "linux" and os.getcwd() == '/usr/local/src'
+if in_container:
+ results_dst_dir = os.path.join(parent_dir, f"valis/tests/docker")
+else:
+ results_dst_dir = os.path.join(parent_dir, f"valis/tests/{sys.version_info.major}{sys.version_info.minor}")
 
 def register_hi_rez(src_dir):
  high_rez_dst_dir = os.path.join(results_dst_dir, "high_rez")
@@ -108,9 +113,9 @@ def register_hi_rez(src_dir):
  registrar.draw_matches(matches_dst_dir)
 
 
-def register_ihc(max_error=45):
+def test_register_ihc(max_error=50):
+ """Tests registration and lossy jpeg2000 compression"""
  ihc_src_dir = os.path.join(datasets_src_dir, "ihc")
- ihc_dst_dir = os.path.join(results_dst_dir, "ihc")
  try:
  registrar = registration.Valis(ihc_src_dir, results_dst_dir)
  rigid_registrar, non_rigid_registrar, error_df = registrar.register()
@@ -122,8 +127,7 @@ def register_ihc(max_error=45):
  assert False, f"error was {avg_error} but should be below {max_error}"
 
  registered_slide_dst_dir = os.path.join(registrar.dst_dir, "registered_slides", registrar.name)
- registrar.warp_and_save_slides(registered_slide_dst_dir)
- # registration.kill_jvm()
+ registrar.warp_and_save_slides(dst_dir=registered_slide_dst_dir, Q=90, compression="jp2k")
 
  # shutil.rmtree(ihc_dst_dir, ignore_errors=True)
 
@@ -138,7 +142,6 @@ def test_register_cycif(max_error=3):
 
 
  cycif_src_dir = os.path.join(datasets_src_dir, "cycif")
- cycif_dst_dir = os.path.join(results_dst_dir, "cycif")
  try:
  registrar = registration.Valis(cycif_src_dir, results_dst_dir)
  rigid_registrar, non_rigid_registrar, error_df = registrar.register()
@@ -155,7 +158,8 @@ def test_register_cycif(max_error=3):
  dst_f = os.path.join(registrar.dst_dir, "registered_slides", f"{registrar.name}.ome.tiff")
  merged_img, channel_names, ome_xml = registrar.warp_and_merge_slides(dst_f,
  channel_name_dict=channel_name_dict,
- drop_duplicates=True)
+ drop_duplicates=True,
+ Q=90)
 
  # registration.kill_jvm()
 
@@ -178,6 +182,8 @@ def test_register_hi_rez_cycif():
  register_hi_rez(src_dir=cycif_src_dir)
 
 
-# if __name__ == "__main__":
-# test_register_hi_rez_ihc()
-# test_register_hi_rez_cycif()
+if __name__ == "__main__" and in_container:
+ # test_register_cycif()
+ # test_register_ihc()
+ test_register_hi_rez_ihc()
+ test_register_hi_rez_cycif()

tests/test_warp_fxns.py

@@ -227,3 +227,7 @@ def test_img_warp(max_mi=0.5, max_px_d=0.1):
  passed = pt_d < max_px_d and mi < max_mi
 
  assert passed
+
+
+if __name__ == "__main__":
+ test_img_warp()

valis/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 from . import affine_optimizer
 from . import feature_detectors

valis/affine_optimizer.py

@@ -308,7 +308,7 @@ def update_joint_H(binned_moving, binned_fixed, H, M, sample_pts, pos=0,
  return H
 
 
-@nba.jit(nopython=False)
+# @nba.jit(nopython=False)
 def get_neighborhood(im, i, j, r):
  """
  Get values in a neighborhood
@@ -317,7 +317,7 @@ def get_neighborhood(im, i, j, r):
  return im[i - r:i + r + 1, j - r:j + r + 1].flatten()
 
 
-@nba.jit(nopython=False)
+# @nba.jit(nopython=False)
 def build_P(A, B, r, mask):
  hood_size = (2 * r + 1) ** 2
  d = 2 * hood_size

valis/registration.py

@@ -19,6 +19,7 @@
 from copy import deepcopy
 from pprint import pformat
 import json
+from colorama import Fore
 
 from . import feature_matcher
 from . import serial_rigid
@@ -973,6 +974,8 @@ def warp_and_save_slide(self, dst_f, level=0, non_rigid=True,
  Q factor for lossy compression
 
  """
+ if src_f is None:
+ src_f = self.src_f
 
  warped_slide = self.warp_slide(level=level, non_rigid=non_rigid,
  crop=crop,
@@ -2103,10 +2106,10 @@ def get_imgs_in_dir(self):
 
  elif len(matching_f) > 1:
  msg = f"found {len(matching_f)} matches for {dir_name}: {', '.join(matching_f)}"
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
  elif len(matching_f) == 0:
  msg = f"Can't find slide file associated with {dir_name}"
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
 
  def set_dst_paths(self):
  """Set paths to where the results will be saved.
@@ -2189,7 +2192,7 @@ def get_slide(self, src_f):
  f"the dictionary. Either key (filenmae) or value (assigned name) will work:\n"
  f"{pformat(possible_names_dict)}")
 
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
  slide_obj = None
 
  return slide_obj
@@ -2233,7 +2236,7 @@ def get_img_names(self, img_list):
  z = len(str(len(dup_paths)))
 
  msg = f"Detected {len(dup_paths)} images that would be named {dup_name}"
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
 
  for j, p in enumerate(dup_paths):
  new_name = f"{names_dict[p]}_{str(j).zfill(z)}"
@@ -2279,15 +2282,15 @@ def convert_imgs(self, series=None, reader_cls=None):
  slide_reader_cls = slide_io.get_slide_reader(f, series=series)
  except Exception as e:
  msg = f"Attempting to get reader for {f} created the following error:\n{e}"
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
  else:
  slide_reader_cls = reader_cls
 
  try:
  reader = slide_reader_cls(f, series=series)
  except Exception as e:
  msg = f"Attempting to read {f} created the following error:\n{e}"
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
 
  slide_dims = reader.metadata.slide_dimensions
  levels_in_range = np.where(slide_dims.max(axis=1) < self.max_image_dim_px)[0]
@@ -2994,7 +2997,7 @@ def rigid_register(self):
 
  if rigid_registrar is False:
  msg = "Rigid registration failed"
- valtils.print_warning(msg)
+ valtils.print_warning(msg, rgb=Fore.RED)
 
  return False
 
@@ -4147,7 +4150,7 @@ def register(self, brightfield_processing_cls=DEFAULT_BRIGHTFIELD_CLASS,
  error_df.to_csv(data_f_out, index=False)
 
  except Exception as e:
- valtils.print_warning(e)
+ valtils.print_warning(e, rgb=Fore.RED)
  print(traceback.format_exc())
  kill_jvm()
  return None, None, None
@@ -4451,7 +4454,7 @@ def warp_and_save_slides(self, dst_dir, level=0, non_rigid=True,
  crop=True,
  colormap=None,
  interp_method="bicubic",
- tile_wh=None, compression="lzw"):
+ tile_wh=None, compression="lzw", Q=100):
 
  f"""Warp and save all slides
 
@@ -4492,6 +4495,9 @@ def warp_and_save_slides(self, dst_dir, level=0, non_rigid=True,
  Compression method used to save ome.tiff . Default is lzw, but can also
  be jpeg or jp2k. See pyips for more details.
 
+ Q : int
+ Q factor for lossy compression
+
  """
  pathlib.Path(dst_dir).mkdir(exist_ok=True, parents=True)
 
@@ -4508,12 +4514,14 @@ def warp_and_save_slides(self, dst_dir, level=0, non_rigid=True,
  valtils.print_warning(msg)
 
  dst_f = os.path.join(dst_dir, slide_obj.name + ".ome.tiff")
+
  slide_obj.warp_and_save_slide(dst_f=dst_f, level=level,
  non_rigid=non_rigid,
  crop=crop,
+ src_f=slide_obj.src_f,
  interp_method=interp_method,
  colormap=slide_cmap,
- tile_wh=tile_wh, compression=compression)
+ tile_wh=tile_wh, compression=compression, Q=Q)
 
  @valtils.deprecated_args(perceputally_uniform_channel_colors="colormap")
  def warp_and_merge_slides(self, dst_f=None, level=0, non_rigid=True,

valis/valtils.py

@@ -11,7 +11,7 @@
 color_init()
 
 
-def print_warning(msg, warning_type=UserWarning, rgb=Fore.RED):
+def print_warning(msg, warning_type=UserWarning, rgb=Fore.YELLOW):
  """Print warning message with color
  """
  warning_msg = f"{rgb}{msg}{Style.RESET_ALL}"