Merge pull request #686 from NEUBIAS/add-py-strings-paths

Added basic implementation for string and path manipulation in python

_includes/string_concat/creating_log_messages.py

@@ -1 +1,16 @@
-# TODO
+# %%
+# Creating log messages
+
+image_index = 11
+num_images = 100
+
+# %%
+# strings can be added together with the '+' operator
+print("Analyzing image " + str(image_index) + "/" + str(num_images) + "...")
+
+# %%
+# An alternative way to combine strings and variables from your code
+# are so called f-strings: in f-strings you can add variables (and some
+# code) in between curly braces. Types are automatically coerced to strings.
+#  The below code achieves the same output.
+print(f"Analysing image {image_index}/{num_images}...")

_includes/string_concat/manipulating_file_paths.ijm

@@ -1,5 +1,18 @@
 // manipulating file paths
 tmpFolder = getDirectory("temp");
+print(tmpFolder);
 fileName = "nuclei.tif";
-path = tmpFolder + File.separator + fileName;
+path = tmpFolder + fileName;
 print(path);
+
+// Let's create a file name for a label image derived from the nuclei.tif
+// such the file name will be nuclei_labels.tif.
+filenameWithoutExtension = File.getNameWithoutExtension(path);
+print(filenameWithoutExtension)
+labelsPath = tmpFolder + filenameWithoutExtension + "_labels.tif";
+print(labelsPath);
+
+// Now we want to create a file name for a .csv file, that shares the
+// file name up to the extension.
+csvPath = tmpFolder + filenameWithoutExtension + ".csv";
+print(csvPath);

_includes/string_concat/manipulating_file_paths.py

@@ -1 +1,38 @@
-# TODO
+# %%
+# Manipulating file paths
+
+import pathlib
+import tempfile
+
+# %%
+# Let's get a folder and a file name to practice with.
+# Temporary folder is different on different operating systems.
+# We use tempfile.gettempdir() from the standard library as it has all that logic.
+tmp_folder = pathlib.Path(tempfile.gettempdir())
+file_name = "nuclei.tif"
+
+# %%
+# Combine folder and file name.
+# pathlib.Path objects support "syntactic sugar", like using '/' as a
+# separator when composing paths.
+image_path = tmp_folder / file_name
+print(image_path)
+
+# %%
+# The parent for a Path object gives you the containing folder
+parent_folder = image_path.parent
+print(parent_folder == tmp_folder)
+
+# %%
+# Let's create a file name for a label image derived from the nuclei.tif
+# such the file name will be nuclei_labels.tif.
+filename_no_extension = image_path.stem
+print(filename_no_extension)
+labels_path = tmp_folder / f"{filename_no_extension}_labels.tif"
+
+# %%
+# Now we want to create a file name for a .csv file, that shares the
+# file name up to the extension.
+# If we only change the extension, we can use the with_suffix method.
+csv_path = image_path.with_suffix(".csv")
+print(csv_path)