Adding TMI (#46)

* using tmi

* pinned tmi to v0.0.1

mibi_bin_tools/bin_files.py

@@ -7,8 +7,8 @@
 import skimage.io as io
 import xarray as xr
 
-from mibi_bin_tools import io_utils, type_utils, _extract_bin
-from tmi.image_utils import save_image
+from mibi_bin_tools import type_utils, _extract_bin
+from tmi import io_utils, image_utils
 
 
 def _mass2tof(masses_arr: np.ndarray, mass_offset: float, mass_gain: float,
@@ -102,7 +102,7 @@ def _write_out(img_data: np.ndarray, out_dir: str, fov_name: str, targets: List[
             # if not replace (i=1), only save intensity images for specified targets
             if i == 0 or (target in list(intensities)):
                 fname = os.path.join(out_dir_i, f"{target}{suffix}.tiff")
-                save_image(fname=fname, data=img_data[i, :, :, j].astype(save_dtype))
+                image_utils.save_image(fname=fname, data=img_data[i, :, :, j].astype(save_dtype))
 
 
 def _find_bin_files(data_dir: str,

mibi_bin_tools/panel_utils.py

@@ -1,7 +1,7 @@
 from typing import Union, List
 import pandas as pd
 
-from mibi_bin_tools.type_utils import make_iterable
+from tmi import misc_utils
 
 
 def make_panel(mass: Union[float, List[float]],
@@ -25,9 +25,9 @@ def make_panel(mass: Union[float, List[float]],
             single mass panel as pandas dataframe
     """
 
-    mass = make_iterable(mass)
+    mass = misc_utils.make_iterable(mass)
     if target_name is not None:
-        target_name = make_iterable(target_name)
+        target_name = misc_utils.make_iterable(target_name)
         if len(mass) != len(target_name):
             raise ValueError(
                 '`mass` and `target_name` did not contain the same number of elements.  '
@@ -38,16 +38,16 @@ def make_panel(mass: Union[float, List[float]],
 
     # check for range lists
     for r in (low_range, high_range):
-        if make_iterable(r) == r:
+        if misc_utils.make_iterable(r) == r:
             if len(r) != len(mass):
                 raise ValueError(
                     '`mass` and a range argument did not contain the same number of elements.  '
                     'If only one integration range is required, `low_range` and `high_range` can '
                     'be set to float values, e.g `low_range=0.3`'
                 )
 
-    low_range = make_iterable(low_range)
-    high_range = make_iterable(high_range)
+    low_range = misc_utils.make_iterable(low_range)
+    high_range = misc_utils.make_iterable(high_range)
 
     if len(low_range) != len(mass):
         low_range = low_range * len(mass)

mibi_bin_tools/type_utils.py

@@ -1,4 +1,5 @@
 from typing import Union, Iterable
+from tmi import misc_utils
 
 
 def any_true(a: Union[bool, Iterable[bool]]) -> bool:
@@ -12,20 +13,4 @@ def any_true(a: Union[bool, Iterable[bool]]) -> bool:
         bool:
             whether any true values where found
     """
-    return any(make_iterable(a))
-
-
-def make_iterable(a: Union[type, Iterable[type]], ignore_str=True) -> Iterable[type]:
-    """ Convert noniterable type to singelton in list
-
-    Args:
-        a (T | Iterable[T]):
-            value or iterable of type T
-        ignore_str (bool):
-            whether to ignore the iterability of the str type
-
-    Returns:
-        List[T]:
-            a as singleton in list, or a if a was already iterable.
-    """
-    return a if hasattr(a, '__iter__') and not (isinstance(a, str) and ignore_str) else [a]
+    return any(misc_utils.make_iterable(a))

requirements.txt

@@ -3,5 +3,5 @@ matplotlib==3.4.3
 numpy>=1.21.6,<2
 pandas>=1.3.5,<2
 scikit-image>=0.19.3,<0.20
-tmi @ git+https://github.com/angelolab/tmi.git
+tmi @ git+https://github.com/angelolab/tmi.git@v0.0.1
 xarray>=2022.6.0,<2023

tests/bin_files_test.py

@@ -9,7 +9,8 @@
 import numpy as np
 import pandas as pd
 
-from mibi_bin_tools import bin_files, io_utils, type_utils, _extract_bin
+from mibi_bin_tools import bin_files, type_utils, _extract_bin
+from tmi import io_utils
 
 THIS_DIR = Path(__file__).parent