Metadata-Version: 2.1
Name: execdmscript
Version: 1.1.3
Summary: A python module for executing DM-Script from python in the Gatan Microscopy Suite® (GMS) (Digital Micrograph)
Home-page: https://github.com/miile7/execdmscript
Author: miile7
Author-email: miile7@gmx.de
License: UNKNOWN
Description: # execdmscript
        
        A Python module for executing DM-Script from Python in 
        [Gatan Microscopy Suite (GMS) (Digital Micrograph) Version 3.4 or later](https://www.gatan.com/products/tem-analysis/gatan-microscopy-suite-software).
        
        **Table of Contents**
        
        1. [Foreword](#foreword)
        2. [Usage](#usage)
        3. [Installation](#installation)
        4. [License and Publications](#license-and-publications)
        
        ## Foreword
        
        This module is created because I needed to use DM-Scripts Dialogs in my project. But this
        project was written in Python. Because there is no Python implementation for dialogs I 
        decided to execute DM-Script that creates the dialogs. But then getting data from one to
        the other programming language was more difficult than I thought. This module tries to 
        solve those problems and hide verything away.
        
        ## Usage
        
        > **Important**:
        > 
        > This module is for running DM-Script scripts **within and only within** the Python 
        > interpreter of a running GMS (DigitalMicrograph). So you must only use this when you 
        > are in a Python script window in GMS (DigitalMicrograph). This **does not work in the 
        > command line!**
        
        After the [installation](#installation) you can execute the following examples. Check out
        the [one glance example](#one-glance-example) if you used this module already and just 
        forgot how it worked. If you have never dealt with Python in GMS or you are new to 
        `execdmscript`, check out the [step by step examples](#step-by-step-examples) below.
        
        ### Step by step examples
        
        The following examples are taken from the *examples* directory which can also be found on 
        the [github page](https://github.com/miile7/execdmscript/tree/master/example).
        
        #### Example 0: Hello World
        
        Because of tradition, let's do the hello world first. Obviously this is a lot more 
        complicated than actually needed, but it teaches the basics.
        
        ```python
        import execdmscript
        
        # set the text in python
        world_text = "Hello World!"
        
        # create an executable dm-script code
        dmscript = """
        OKDialog(text);
        result(text);
        """
        
        # save which variables should be passed from python to dm-script and how they should be 
        # called
        setvars = {
        	"text": world_text
        }
        
        # execute the script
        with execdmscript.exec_dmscript(dmscript, setvars=setvars):
        	pass
        ```
        
        #### Example 1: Getting started
        
        After the [installation](#installation) open GMS (DigitalMicrograph). Create a new script
        window (<kbd>Ctrl</kbd> + <kbd>K</kbd>) and make sure it is set to *Python*  as the 
        scripting language. For this example it does not matter if the script is executed in the 
        background or not. Now type in (or copy) the following code:
        
        ```python
        import execdmscript
        
        # `a` and `b` are given in python
        a = 10
        b = 20
        
        # This is the dm-script to execute
        dmscript = "number c = a + b;"
        
        # This are the variables the upper dm-script will know
        setvars = {"a": a, "b": b}
        
        # This are the variables this python script will know after the execution
        readvars = {"c": int}
        
        with execdmscript.exec_dmscript(dmscript, setvars=setvars, readvars=readvars) as script:
        	# now we can access `c` because it is set in the `readvars`
        	print(script["c"])
        ```
        
        This script calculates `a` + `b`. But `a` and `b` are Python variables while `c` is a 
        variable created in dm-script.
        
        The `setvars` is a `dict` that takes the variable name as the key and the variable value
        as its value. These values with their names will be accessable in the executed dm-script.
        Values of the types `int`, `float`, `bool`, `str`, `list` and `dict` are
        supported. They will be converted to their dm-script equivalent. This means `int`, `float`
        and `bool` will be of the type `number`. `str` will be `string`. And `list` and `dict` 
        will both be `TagGroup`s but the former will be a `TagList` and the latter will be a 
        "true" `TagGroup`.
        
        The `readvars` is a `dict` that takes the dm-script variable name as the key and the type
        to expect as the value. This means that all the variables that have a key in the 
        `readvars` and are defined in the executed dm-script will later be accessable in Python.
        
        #### Example 2: Outhouse code
        
        > **Important**:
        > 
        > When you are trying the example code, make sure you always know the complete path of 
        > the dm-script *.s file in your Python script. It is not enough to have the file name 
        > only!
        
        Now let's go a little bit more complicated. There is no need to execute a sum operation in
        dm-script.
        
        This time we will create two files. The first one will be a dm-script file, the second one
        will be a Python file again.
        
        Open GMS and create a new dm-script window. Enter the following code and save it to 
        somewhere where it is easy to find, say `C:\testdmscript2.s`.
        
        ```c
        TagGroup dlg, dlg_items, field;
        
        dlg = DLGCreateDialog("Headlines of website", dlg_items);
        
        // Note that the `text` is neither initialized nor declared, that is important as it will
        // be done by the python script!
        field = DLGCreateLabel(text);
        field.DLGWidth(100);
        field.DLGHeight(4);
        
        dlg.DLGAddElement(field);
        
        alloc(UIFrame).init(dlg).pose();
        ```
        
        As said, save the file somewhere, say `C:\testdmscript2.s`.
        
        Now open a new Python script window in GMS. Create the following code:
        
        ```python
        import execdmscript
        
        import urllib.request
        import html.parser
        import re
        
        # get the text of example.com
        content = str(urllib.request.urlopen("https://www.example.com/").read())
        
        # get all headlines
        matches = re.findall(r"<h([\d])>([^<]+)</h\1>", content)
        if matches is not None:
        	headlines = [x[1] for x in matches]
        	text = "Headlines:\n- " + "\n- ".join(headlines)
        else:
        	headlines = []
        	text = "*No headlines found*"
        
        # Tell the dm-script the variables it should know
        setvars = {"text": text}
        
        # set your filepath, needs to be the complete path, not just the name!
        path = r"C:\testdmscript2.s"
        
        with execdmscript.exec_dmscript(path, setvars=setvars):
        	pass
        ```
        
        This will create a dm-script dialog that shows all headlines of the website stated in the
        code, in this case `example.com`.
        
        This time the dm-script is in a separate file which is strongly recommended. This way the 
        dm-script file can be debugged a lot easier. Also the code is better to read and 
        structured in a better way.
        
        Also as one can see, this are just a few Python lines but will be very hard to get with 
        pure dm-script. On the other hand there no GMS-dialogs in Python.
        
        #### Example 3: TagGroups and TagLists
        
        > **Important**:
        > 
        > When you are trying the example code, make sure you always know the complete path of 
        > the dm-script *.s file in your Python script. It is not enough to have the file name 
        > only!
        
        While Python has `list`s and `dict`s (and a lot more of course) for dealing with multiple
        values, dm-script does that with `TagList`s and `TagGroup`s. Both are more less equivalent
        even though the handling is very different. Therefore `execdmscript` converts both types
        automatically.
        
        Open GMS again and create a new Python script window. Create the following code:
        
        ```c
        TagGroup dlg, dlg_items, wrapper, inputs;
        
        dlg = DLGCreateDialog("Add text to the headlines", dlg_items);
        wrapper = DLGCreateGroup();
        wrapper.DLGTableLayout(2, headlines.TagGroupCountTags(), 0);
        
        inputs = NewTagList();
        for(number i = 0; i < headlines.TagGroupCountTags(); i++){
        	string text;
        	if(headlines.TagGroupGetIndexedTagAsString(i, text)){
        		TagGroup label = DLGCreateLabel("Text for " + text, 25);
        		wrapper.DLGAddElement(label);
        		
        		TagGroup input = DLGCreateStringField("");
        		input.DLGIdentifier("input-" + i);
        		wrapper.DLGAddElement(input);
        		inputs.TagGroupInsertTagAsTagGroup(infinity(), input);
        	}
        }
        
        dlg.DLGAddElement(wrapper);
        
        object dialog = alloc(UIFrame).init(dlg);
        
        // make sure the variable always exists, it may be empty but 
        // it has to be declared!
        TagGroup headline_texts = NewTagList();
        
        if(dialog.pose()){
        	for(number i = 0; i < headlines.TagGroupCountTags(); i++){
        		string text;
        		if(headlines.TagGroupGetIndexedTagAsString(i, text)){
        			TagGroup input;
        			inputs.TagGroupGetIndexedTagAsTagGroup(i, input);
        			
        			TagGroup vals = NewTagGroup();
        			vals.TagGroupCreateNewLabeledTag("headline");
        			vals.TagGroupSetTagAsString("headline", text);
        			
        			vals.TagGroupCreateNewLabeledTag("text");
        			vals.TagGroupSetTagAsString("text", input.DLGGetStringValue());
        			
        			headline_texts.TagGroupInsertTagAsTagGroup(infinity(), vals);
        		}
        	}
        }
        ```
        
        This creates a dialog that shows all headlines in the `headlines` `TagList` and allows to
        add texts to them. Save this file with any name, say `C:\testdmscript3.s`.
        
        Now open a new Python script window in GMS. Create the following code:
        
        ```python
        import execdmscript
        
        headlines = [
        	"Section 1",
        	"Section 2", 
        	"Section 3"
        ]
        
        # Tell the dm-script the variables it should know
        setvars = {"headlines": headlines}
        
        # Get the list of headlines
        readvars = {"headline_texts": list}
        
        # set your filepath, needs to be the complete path, not just the name!
        path = r"C:\testdmscript3.s"
        
        text = ""
        with execdmscript.exec_dmscript(path, setvars=setvars, readvars=readvars) as script:
        	for section in script["headline_texts"]:
        		text += "**{}**\n{}\n\n".format(section["headline"], section["text"])
        
        if text != "":
        	print(text)
        else:
        	print("Could not find any sections.")
        ```
        
        The `script["headline_texts"]` is a list containing `dict`s because `TagList`s are 
        converted to `list`s automatically and `TagGroup`s to `dict`s.
        
        #### Example 4: Debug your code
        
        The downside of using combined scripts is that one cannot really see what the dm-script 
        interpreter is actually doing. For this problem there is a debug mode. Simply use
        `execdmscript.exec_dmscript(code, debug=True, debug_file=file_path)` to get the dm-script
        file that normally would be executed.
        
        Let's assume that the file `C:\testdmscript4.s` exists and contains any code (if you want 
        you can create this file and see what happens). To debug the complete file check out the 
        following example Python code:
        
        ```python
        import execdmscript
        
        # Tell the dm-script the variables it should know
        setvars = {"variable1": 1, "variable2": "B", "variable3": False}
        
        # Get the list of headlines
        readvars = {"variable4": str, "variable5": int}
        
        # set your filepath, needs to be the complete path, not just the name!
        path = r"C:\testdmscript4.s"
        
        with execdmscript.exec_dmscript(path, setvars=setvars, readvars=readvars, debug=True,
        								debug_file=r"C:\debugfile.s") as script:
        	pass
        ```
        
        This code will not execute dm-script code! But it will instead create the file at 
        `C:\debugfile.s` that includes all the synchronization mechanisms that the `setvars` and
        `readvars` need to work. This way you may find and fix bugs. Note that the `debug_file` 
        is ignored when `debug` is not `True`.
        
        #### Example 5: Multiple Scripts
        
        Sometimes it is useful to structure your dm-script code too, especially if you have bigger
        files to include. You can add as many dm-scripts directly or as files as you want. Note 
        that the `readvars` and the `setvars` will be defined before and after all scripts. So you 
        must not use variable names in one of the scripts that are in the `setvars` and all 
        variables in the `readvars` have to be delcared in exactly one file (not all `readvars` 
        have to be in the same file.
        
        Create the dm-script file `C:\testdmscript5.s` with the following content:
        ```c
        number e = d + b;
        ```
        
        Now create a new Python script with this code:
        ```python
        import execdmscript
        
        dmscript1 = "number c = a + b;"
        dmscript2 = "number d = c + a;"
        dmscript3 = r"C:\testdmscript5.s"
        
        setvars = {"a": 1, "b": 2}
        readvars = {"c": int, "d": int, "e": int}
        
        with execdmscript.exec_dmscript(dmscript1, dmscript2, dmscript3, setvars=setvars, 
        								readvars=readvars) as script:
        	print("c:", script["c"])
        	print("d:", script["d"])
        	print("e:", script["e"])
        ```
        
        #### More Examples
        
        For more examples check out the github page. There you can find the following example 
        scripts with more complicated behaviour:
        
        - example_separate_thread.py: Show the `separate_thread` parameter of 
          `execdmscript.exec_dmscript()` by creating a progress dialog with dm-script that shows 
          the progress a python thread does
        - example_combined.py: Show multiple scripts with a more complicated situation, this 
          basically takes all above scenes in one example
        
        ### One glance example
        
        The following example shows the basic usage:
        
        ```python
        try:
        	from execdmscript import exec_dmscript
        
        	# some script to execute
        	script = "OKDialog(start_message)"
        	script_file = "path/to/script.s"
        
        	# variables that will be defined for the scripts (and readable later on in Python)
        	sv = {"start_message": "Starting now!"}
        	# variables the dm-script defines and that should be readable in the Python file
        	rv = {"selected_images": list,
        		"options": "TagGroup",
        		"show_message": "nUmBeR"}
        
        	with exec_dmscript(script, script_file, readvars=rv, setvars=sv) as script:
        		# all variables can be accessed via indexing `script` or by using 
        		# `script.synchronized_vars`, note that `script` is also iterable like a dict
        		print(script["start_message"])
        		print(script["selected_images"])
        		print(script["options"])
        		print(script["show_message"])
        
        except Exception as e:
        	# dm-script error messages only show the error type but not the message
        	print("Exception: ", e)
        
        	import traceback
        	traceback.print_exc()
        ```
        
        ### Example execution without installation
        
        If you want to try out the module or if you don't want to install it, make sure to add the 
        import path to `sys.path`. You can add the path manually:
        
        ```python
        import os
        import sys
        
        # add the path to the execdmscript directory (so in execdmscript-dir there is the file 
        # __init__.py and the file execdmscript.py)
        sys.path.insert(0, "path/to/execdmscript-dir/")
        ```
        
        If you only know the path relatively to your executing file, you can find the `__file__` 
        (which does not exist in GMS) like the following code:
        
        ```python
        try:
        	import DigitalMicrograph as DM
        	in_digital_micrograph = True
        except ImportError:
        	in_digital_micrograph = False
        
        file_is_missing = False
        try:
        	if __file__ == "" or __file__ == None:
        		file_is_missing = True
        except NameError:
        	file_is_missing = True
        
        if in_digital_micrograph and file_is_missing:
        	# the name of the tag is used, this is deleted so it shouldn't matter anyway
        	file_tag_name = "__python__file__"
        	# the dm-script to execute, double curly brackets are used because of the 
        	# python format function
        	script = ("\n".join((
        		"DocumentWindow win = GetDocumentWindow(0);",
        		"if(win.WindowIsvalid()){{",
        			"if(win.WindowIsLinkedToFile()){{",
        				"TagGroup tg = GetPersistentTagGroup();",
        				"if(!tg.TagGroupDoesTagExist(\"{tag_name}\")){{",
        					"number index = tg.TagGroupCreateNewLabeledTag(\"{tag_name}\");",
        					"tg.TagGroupSetIndexedTagAsString(index, win.WindowGetCurrentFile());",
        				"}}",
        				"else{{",
        					"tg.TagGroupSetTagAsString(\"{tag_name}\", win.WindowGetCurrentFile());",
        				"}}",
        			"}}",
        		"}}"
        	))).format(tag_name=file_tag_name)
        
        	# execute the dm script
        	DM.ExecuteScriptString(script)
        
        	# read from the global tags to get the value to the python script
        	global_tags = DM.GetPersistentTagGroup()
        	if global_tags.IsValid():
        		s, __file__ = global_tags.GetTagAsString(file_tag_name);
        		if s:
        			# delete the created tag again
        			DM.ExecuteScriptString(
        				"GetPersistentTagGroup()." + 
        				"TagGroupDeleteTagWithLabel(\"{}\");".format(file_tag_name)
        			)
        		else:
        			del __file__
        
        	try:
        		__file__
        	except NameError:
        		# set a default if the __file__ could not be received
        		__file__ = ""
        
        import os
        import sys
        
        if __file__ != "":
        	# add the parent directory to the system path so the execdmscript file
        	# can be imported
        	base_path = str(os.path.dirname(os.path.dirname(__file__)))
        	
        	if base_path not in sys.path:
        		sys.path.insert(0, base_path)
        
        import execdmscript
        ```
        
        The upper code works for file structures like
        ```
        + base
        |   + execdmscript
        |   |   - __init__.py
        |   |   - execdmscript.py
        |   + code
        |   |   - your-file-with-the-upper-code.py
        ```
        
        
        ## Installation
        
        ### Via PIP (Recommended)
        
        You can install `execdmscript` via [PyPI](https://pypi.org/project/execdmscript/). To 
        install it into the GMS virtual Python environment execute the following commands:
        
        ```cmd
        conda activate GMS_VENV_Python
        Python -m pip install execdmscript
        ```
        
        ### Manually
        
        To manually install `execdmscript` download the `execdmscript` directory (the one that 
        contains the `__init__.py` and the `execdmscript.py`) and install them
        
        1. *Recommended if manually* in one of the GMS plugin directories by
            1. using the *File* Menu and then click on *Install Script File* 
               (Check out GMS Help in the chapter *Scripting* > *Installing Scripts and Plugins*) 
               *or*
            2. placing the `execdmscript` directory in the plugin directory manually. Plugin 
               directories are `C:\Users\UserName\AppData\Local\Gatan\Plugins` or in 
               `C:\InstallationDir\Gatan\Plugins`. To find all plugin directories execute the 
               following code:
               ```c
               string dirs = "Plugin Directories:\n\n"; 
               string dir;
               
                for(number i = 1011; i >= 1008; i--){
                    try{
                        dir = GetApplicationDirectory(i, 0);
                        dirs += dir + "\n"
                    }
                    catch{
                        break;
                    }
                }
        
                result(dirs);
                OKDialog(dirs);
                ```
               *or*
        1. in the miniconda plugin directory (On windows normally in 
           `%ProgramData%\Miniconda3\envs\GMS_VENV_PYTHON\Lib\site-packages`, then place the 
           `execdmscript` directory here)
        
        ## License and Publications
        
        This module is licensed under [Mozilla Public License](https://www.mozilla.org/en-US/MPL/2.0/).
        
        This means you can use the code for whatever you want. But please do not publish my code 
        as your work.
        
        If you want to publish papers, do so. There is no need to cite me. If you still want to 
        cite me (for any reason), please contact me via Github. For any questions please also 
        contact me on Github.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Python: >=3.5
Description-Content-Type: text/markdown
